#SampleID	BarcodeSequence	LinkerPrimerSequence	barcode_read_group_tag	dna_extracted_prep	experiment_alias	experiment_center	experiment_design_description	experiment_title	key_seq	library_construction_protocol	linker	nucl_acid_amp	nucl_acid_ext	pcr_cond	pcr_primers	physical_specimen_remaining_prep	platform	pool_member_name	pool_proportion	primer_read_group_tag	region	run_alias	run_center	run_date	run_prefix	samp_collect_device_prep	samp_size	sample_center	sample_type_prep	sequencing_meth	study_center	study_ref	target_gene	target_subfragment	url	age	age_unit	altitude	anatomical_sample_site	anonymized_name	assigned_from_geo	body_habitat	body_product	body_site	collection_date	common_name	common_sample_site	country	depth	dna_extracted	elevation	env_biome	env_feature	env_matter	hiv	host_common_name	host_individual	host_subject_id	host_taxid	latitude	longitude	original_sample_site	physical_specimen_remaining	public	samp_collect_device	sample_type	sex	taxon_id	title	qiita_study_title	qiita_study_alias	qiita_owner	qiita_principal_investigator	Description
449.M22Indr	CGAGCAGCACAT	CATGCTGCCTCCCGTAGGAGT	M22Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Indr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right index finger	sample366	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M14Fotl	GACGATATCGCG	CATGCTGCCTCCCGTAGGAGT	M14Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left foot surface	sample236	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Nstr	GCAGGATAGATA	CATGCTGCCTCCCGTAGGAGT	F31Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Nstr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample375	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F11Labi	AGATGTTCTGCT	CATGCTGCCTCCCGTAGGAGT	F11Labi	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Labi	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Frenulum of labia minora	sample087	False	UBERON:skin	UBERON:mucus	UBERON:labia minora	2008-2009	human skin metagenome	labia minora	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:mucus	Negative	human	F1	F1	9606	40.0149856	-105.2705456	labia minora	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Indl	CGAGAGTTACGC	CATGCTGCCTCCCGTAGGAGT	M22Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Indl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left index finger	sample144	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M14Fotr	GACGAGTCAGTC	CATGCTGCCTCCCGTAGGAGT	M14Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right foot surface	sample459	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M14Fcsw	GACTAGACCAGC	CATGCTGCCTCCCGTAGGAGT	M14Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample499	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M1	M1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M33Plmr	GCTGTAGTATGC	CATGCTGCCTCCCGTAGGAGT	M33Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample434	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M54Ewax	TAGCTGAGTCCA	CATGCTGCCTCCCGTAGGAGT	M54Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:External auditory canal	sample312	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M5	M5	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M12Indr	ACGTGCCGTAGA	CATGCTGCCTCCCGTAGGAGT	M12Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Indr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right index finger	sample364	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Indl	ACGTGAGAGAAT	CATGCTGCCTCCCGTAGGAGT	M12Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Indl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left index finger	sample142	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Ewxl	CTAGCGAACATC	CATGCTGCCTCCCGTAGGAGT	M32Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Ewxl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left external auditory canal	sample186	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M32Hair	CTCAGTATGCAG	CATGCTGCCTCCCGTAGGAGT	M32Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Hair	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Head hair	sample084	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.F11Urin	AGCTCTCAGAGG	CATGCTGCCTCCCGTAGGAGT	F11Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Urin	0.006	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample553	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F1	F1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M64Urin	TCAGTACGAGGC	CATGCTGCCTCCCGTAGGAGT	M64Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Urine	sample602	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M6	M6	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M12Navl	ACTACAGCCTAT	CATGCTGCCTCCCGTAGGAGT	M12Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Navl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Umbilicus	sample273	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Kner	CTAGAGACTCTT	CATGCTGCCTCCCGTAGGAGT	M32Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Kner	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right popliteal fossa	sample340	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Aptr	CTGGACTCATAG	CATGCTGCCTCCCGTAGGAGT	M41Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Aptr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right axilla	sample327	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Fotr	GACGAGTCAGTC	CATGCTGCCTCCCGTAGGAGT	M41Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Fotr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right foot surface	sample468	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Mout	CATAGCGAGTTC	CATGCTGCCTCCCGTAGGAGT	M21Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Mout	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Oral cavity	sample261	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M2	M2	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M64Fcsw	TCAGTGACGTAC	CATGCTGCCTCCCGTAGGAGT	M64Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Feces	sample520	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M6	M6	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M14Plml	GACAGTTACTGC	CATGCTGCCTCCCGTAGGAGT	M14Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left palm	sample204	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Plml	AGCCATACTGAC	CATGCTGCCTCCCGTAGGAGT	F11Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Plml	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample189	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Navl	ATGACCATCGTG	CATGCTGCCTCCCGTAGGAGT	F21Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Navl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Umbilicus	sample269	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Plmr	AGCGACTGTGCA	CATGCTGCCTCCCGTAGGAGT	F11Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Plmr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample412	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M14Plmr	GACAGGAGATAG	CATGCTGCCTCCCGTAGGAGT	M14Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right palm	sample427	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F13Ewax	GAGACAGCTTGC	CATGCTGCCTCCCGTAGGAGT	F13Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External auditory canal	sample297	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F1	F1	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M32Knel	CTAGAACGCACT	CATGCTGCCTCCCGTAGGAGT	M32Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Knel	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left popliteal fossa	sample118	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Aptl	CTGCTGCGAAGA	CATGCTGCCTCCCGTAGGAGT	M41Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Aptl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left axilla	sample105	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Plml	ACATGATCGTTC	CATGCTGCCTCCCGTAGGAGT	M11Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Plml	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left palm	sample201	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M63Ewax	TATGGCACACAC	CATGCTGCCTCCCGTAGGAGT	M63Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:External auditory canal	sample313	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M6	M6	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M12Knel	ACGAGTGCTATC	CATGCTGCCTCCCGTAGGAGT	M12Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Knel	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left popliteal fossa	sample114	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M23Plmr	GATCAGAAGATG	CATGCTGCCTCCCGTAGGAGT	M23Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right palm	sample430	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Plmr	GCTGTGTAGGAC	CATGCTGCCTCCCGTAGGAGT	F32Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Plmr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample421	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Plml	CATCGTATCAAC	CATGCTGCCTCCCGTAGGAGT	M21Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Plml	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left palm	sample205	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Nose	GAGCTGGCTGAT	CATGCTGCCTCCCGTAGGAGT	M42Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Nose	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:External nose	sample032	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Plml	GCTGTAGTATGC	CATGCTGCCTCCCGTAGGAGT	F32Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Plml	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample198	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Plmr	CATCTGTAGCGA	CATGCTGCCTCCCGTAGGAGT	M21Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Plmr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right palm	sample428	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Frhd	ATCGTACAACTC	CATGCTGCCTCCCGTAGGAGT	F21Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Frhd	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Forehead	sample037	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Mout	GAAGCTACTGTC	CATGCTGCCTCCCGTAGGAGT	M41Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Mout	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Oral cavity	sample265	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M4	M4	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M22Nose	CGAGTTGTAGCG	CATGCTGCCTCCCGTAGGAGT	M22Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Nose	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:External nose	sample028	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Kner	ACGATGCGACCA	CATGCTGCCTCCCGTAGGAGT	M12Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Kner	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right popliteal fossa	sample336	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M23Plml	GATCCGACACTA	CATGCTGCCTCCCGTAGGAGT	M23Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left palm	sample207	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Plmr	ACATGTCACGTG	CATGCTGCCTCCCGTAGGAGT	M11Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Plmr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right palm	sample424	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Mout	CTCCTACTGTCT	CATGCTGCCTCCCGTAGGAGT	M32Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Mout	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Oral cavity	sample264	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M3	M3	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M21Pinl	CATGAGTGCTAC	CATGCTGCCTCCCGTAGGAGT	M21Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Pinl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of left pinna	sample170	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F34Fotr	GTCTCATGTAGG	CATGCTGCCTCCCGTAGGAGT	F34Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample455	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Labi	CACATCTAACAC	CATGCTGCCTCCCGTAGGAGT	F22Labi	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Labi	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Frenulum of labia minora	sample090	False	UBERON:skin	UBERON:mucus	UBERON:labia minora	2008-2009	human skin metagenome	labia minora	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:mucus	Negative	human	F2	F2	9606	40.0149856	-105.2705456	labia minora	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M33Urin	GGCGTACTGATG	CATGCTGCCTCCCGTAGGAGT	M33Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Urin	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample588	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M3	M3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M33Uric	GGCTATGACATC	CATGCTGCCTCCCGTAGGAGT	M33Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample587	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M3	M3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M31Fcsp	CGTAAGTCTACT	CATGCTGCCTCCCGTAGGAGT	M31Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Fcsp	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample506	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M3	M3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M21Urin	CATTCGATGACT	CATGCTGCCTCCCGTAGGAGT	M21Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Urin	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample563	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M2	M2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M42Mout	GAGCAGATGCCT	CATGCTGCCTCCCGTAGGAGT	M42Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Mout	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Oral cavity	sample266	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M4	M4	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M21Nstr	CATCATGAGGCT	CATGCTGCCTCCCGTAGGAGT	M21Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Nstr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample379	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M31Fcsw	CGTACAGTTATC	CATGCTGCCTCCCGTAGGAGT	M31Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Fcsw	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample507	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M3	M3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M34Knee	GTACGGCATACG	CATGCTGCCTCCCGTAGGAGT	M34Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Popliteal fossa	sample012	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Glns	ACACTAGATCCG	CATGCTGCCTCCCGTAGGAGT	M11Glns	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Glns	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Glans penis	sample065	False	UBERON:skin	UBERON:sebum	UBERON:glans penis	2008-2009	human skin metagenome	glans penis	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	glans penis	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F14Fotl	GAGTGAGTACAA	CATGCTGCCTCCCGTAGGAGT	F14Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample224	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Kner	AGAACACGTCTC	CATGCTGCCTCCCGTAGGAGT	F11Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Kner	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right popliteal fossa	sample329	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M63Fcsw	TCACAGATCCGA	CATGCTGCCTCCCGTAGGAGT	M63Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Feces	sample519	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M6	M6	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F14Fotr	GAGTCTGAGTCT	CATGCTGCCTCCCGTAGGAGT	F14Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample447	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Navl	ACAGCTAGCTTG	CATGCTGCCTCCCGTAGGAGT	M11Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Navl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Umbilicus	sample272	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Nstl	CATCAGCGTGTA	CATGCTGCCTCCCGTAGGAGT	M21Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Nstl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample157	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M33Fotr	GGACGTCACAGT	CATGCTGCCTCCCGTAGGAGT	M33Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample466	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M33Tong	GGCGACATGTAC	CATGCTGCCTCCCGTAGGAGT	M33Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample543	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M3	M3	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M11Nstl	ACAGTTGCGCGA	CATGCTGCCTCCCGTAGGAGT	M11Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Nstl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample155	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F33Fotr	GTATGTTGCTCA	CATGCTGCCTCCCGTAGGAGT	F33Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample454	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Nstr	ACATCACTTAGC	CATGCTGCCTCCCGTAGGAGT	M11Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Nstr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample377	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F33Fotl	GTCAACGCGATG	CATGCTGCCTCCCGTAGGAGT	F33Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample231	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Fcsw	ATCGATCTGTGG	CATGCTGCCTCCCGTAGGAGT	F21Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Fcsw	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample483	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F2	F2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M23Nost	GATCGTCCAGAT	CATGCTGCCTCCCGTAGGAGT	M23Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample287	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F21Fcsp	ATCCTCAGTAGT	CATGCTGCCTCCCGTAGGAGT	F21Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Fcsp	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample482	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F2	F2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M63Tong	TATTCGTGTCAG	CATGCTGCCTCCCGTAGGAGT	M63Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Dorsal surface of tongue	sample551	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M6	M6	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F24Fcsw	GCTGGTATCTGA	CATGCTGCCTCCCGTAGGAGT	F24Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample487	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F2	F2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F12Pinr	ATACGTCTTCGA	CATGCTGCCTCCCGTAGGAGT	F12Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Pinr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right pinna	sample386	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Tong	CTACATCTAAGC	CATGCTGCCTCCCGTAGGAGT	M31Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Tong	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample541	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M3	M3	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F32Indl	GCTAGTCTGAAC	CATGCTGCCTCCCGTAGGAGT	F32Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Indl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left index finger	sample140	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Pinl	CTCTGCTAGCCT	CATGCTGCCTCCCGTAGGAGT	M32Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Pinl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left pinna	sample173	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F34Urin	GTCTTCGTCGCT	CATGCTGCCTCCCGTAGGAGT	F34Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample578	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F3	F3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F24Nost	GCTAGATGCCAG	CATGCTGCCTCCCGTAGGAGT	F24Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample282	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M31Forr	CGTAGAACGTGC	CATGCTGCCTCCCGTAGGAGT	M31Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Forr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right arm	sample353	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F24Plml	GCGTTACACACA	CATGCTGCCTCCCGTAGGAGT	F24Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left palm	sample196	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F34Uric	GTGACCTGATGT	CATGCTGCCTCCCGTAGGAGT	F34Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample577	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F3	F3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M64Plml	TCACTATGGTCA	CATGCTGCCTCCCGTAGGAGT	M64Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Left palm	sample220	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M63Knee	TATCTCGAACTG	CATGCTGCCTCCCGTAGGAGT	M63Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Popliteal fossa	sample017	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Urin	ATAGGCGATCTC	CATGCTGCCTCCCGTAGGAGT	F12Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Urin	0.006	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample554	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F1	F1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F24Plmr	GCGTATCTTGAT	CATGCTGCCTCCCGTAGGAGT	F24Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right palm	sample419	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Forl	CGTACTAGACTG	CATGCTGCCTCCCGTAGGAGT	M31Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Forl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left arm	sample131	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M34Nost	GTACAAGAGTGA	CATGCTGCCTCCCGTAGGAGT	M34Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample290	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M32Fcsp	CTAGTCAGCTGA	CATGCTGCCTCCCGTAGGAGT	M32Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Fcsp	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample508	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M3	M3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M13Tong	GAAGTCTCGCAT	CATGCTGCCTCCCGTAGGAGT	M13Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Dorsal surface of tongue	sample535	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M1	M1	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M32Fcsw	CTATAGTCGTGT	CATGCTGCCTCCCGTAGGAGT	M32Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Fcsw	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample509	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M3	M3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F32Indr	GCTATCACGAGT	CATGCTGCCTCCCGTAGGAGT	F32Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Indr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right index finger	sample362	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Pinr	CTGAACGCTAGT	CATGCTGCCTCCCGTAGGAGT	M32Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Pinr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right pinna	sample396	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Tong	CATGTCTCTCCG	CATGCTGCCTCCCGTAGGAGT	M21Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Tong	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Dorsal surface of tongue	sample537	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M2	M2	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M11Frhd	ACACGGTGTCTA	CATGCTGCCTCCCGTAGGAGT	M11Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Frhd	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Forehead	sample045	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M14Tong	GACGCTAGTTCA	CATGCTGCCTCCCGTAGGAGT	M14Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Dorsal surface of tongue	sample536	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M1	M1	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F24Knee	GCTAGTCTGAAC	CATGCTGCCTCCCGTAGGAGT	F24Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Popliteal fossa	sample004	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Frhd	CGACAGCTGACA	CATGCTGCCTCCCGTAGGAGT	M22Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Frhd	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Forehead	sample050	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Indl	GAGAGCTCTACG	CATGCTGCCTCCCGTAGGAGT	M42Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Indl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left index finger	sample148	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Forl	CTATCAGTGTAC	CATGCTGCCTCCCGTAGGAGT	M32Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Forl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left arm	sample132	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Pinr	CGTTCGCATAGA	CATGCTGCCTCCCGTAGGAGT	M31Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Pinr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right pinna	sample395	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M64Uric	TCAGTCGACGAG	CATGCTGCCTCCCGTAGGAGT	M64Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Urine	sample601	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M6	M6	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F12Aptr	AGCTTGACAGCT	CATGCTGCCTCCCGTAGGAGT	F12Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Aptr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right axilla	sample316	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Pinr	TGCGCGAATACT	CATGCTGCCTCCCGTAGGAGT	F11Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Pinr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right pinna	sample385	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Nose	CACGGACTATAC	CATGCTGCCTCCCGTAGGAGT	F22Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Nose	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:External nose	sample022	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M33Plml	GCTGTGTAGGAC	CATGCTGCCTCCCGTAGGAGT	M33Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample211	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Pinl	AGCGAGCTATCT	CATGCTGCCTCCCGTAGGAGT	F11Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Pinl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left pinna	sample163	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Aptl	AGCTGACTAGTC	CATGCTGCCTCCCGTAGGAGT	F12Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Aptl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left axilla	sample094	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Fotr	CTACACAAGCAC	CATGCTGCCTCCCGTAGGAGT	M31Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Fotr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample464	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Pinl	CGTTATGTACAC	CATGCTGCCTCCCGTAGGAGT	M31Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Pinl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left pinna	sample172	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Fotl	CTAACGCAGTCA	CATGCTGCCTCCCGTAGGAGT	M31Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Fotl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample241	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M14Nost	GACCACTACGAT	CATGCTGCCTCCCGTAGGAGT	M14Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample286	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F31Forr	GATGTCGTGTCA	CATGCTGCCTCCCGTAGGAGT	F31Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Forr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right arm	sample347	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Forl	GATGCATGACGC	CATGCTGCCTCCCGTAGGAGT	F31Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Forl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left arm	sample125	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M23Knee	GATCTATCCGAG	CATGCTGCCTCCCGTAGGAGT	M23Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Popliteal fossa	sample009	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Indl	ACAGACCACTCA	CATGCTGCCTCCCGTAGGAGT	M11Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Indl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left index finger	sample141	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M43Frhd	GTGCAATCGACG	CATGCTGCCTCCCGTAGGAGT	M43Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Forehead	sample059	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Urin	ACTGTACGCGTA	CATGCTGCCTCCCGTAGGAGT	M12Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Urin	0.006	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample558	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M1	M1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M31Mout	CGTCGATCTCTC	CATGCTGCCTCCCGTAGGAGT	M31Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Mout	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Oral cavity	sample263	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M3	M3	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F21Ewxl	ATCAGGCGTGTG	CATGCTGCCTCCCGTAGGAGT	F21Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Ewxl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left external auditory canal	sample178	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M64Knee	TCAGACAGACCG	CATGCTGCCTCCCGTAGGAGT	M64Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Popliteal fossa	sample018	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M33Ewax	GGCAGTGTATCG	CATGCTGCCTCCCGTAGGAGT	M33Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External auditory canal	sample307	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M3	M3	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F23Knee	GCCACTGATAGT	CATGCTGCCTCCCGTAGGAGT	F23Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Popliteal fossa	sample003	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Glns	GAGACAGCTTGC	CATGCTGCCTCCCGTAGGAGT	M42Glns	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Glns	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Glans penis	sample072	False	UBERON:skin	UBERON:sebum	UBERON:glans penis	2008-2009	human skin metagenome	glans penis	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	glans penis	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Forr	GCGTTACACACA	CATGCTGCCTCCCGTAGGAGT	F32Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Forr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right arm	sample348	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Plml	CTCTCTACCTGT	CATGCTGCCTCCCGTAGGAGT	M32Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Plml	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample210	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Plml	CGTGTGATCAGG	CATGCTGCCTCCCGTAGGAGT	M31Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Plml	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample209	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Forr	CAAGATCGACTC	CATGCTGCCTCCCGTAGGAGT	F22Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Forr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of right arm	sample346	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Plmr	CGTTACTAGAGC	CATGCTGCCTCCCGTAGGAGT	M31Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Plmr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample432	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Forl	CAACTCATCGTA	CATGCTGCCTCCCGTAGGAGT	F22Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Forl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of left arm	sample124	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Fcsw	ACGCTATCTGGA	CATGCTGCCTCCCGTAGGAGT	M12Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Fcsw	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample497	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M1	M1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M12Fcsp	ACGCGCAGATAC	CATGCTGCCTCCCGTAGGAGT	M12Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Fcsp	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample496	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M1	M1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M63Fotl	TATGCGAGGTCG	CATGCTGCCTCCCGTAGGAGT	M63Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Left foot surface	sample251	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Indr	ACAGAGTCGGCT	CATGCTGCCTCCCGTAGGAGT	M11Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Indr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right index finger	sample363	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Forl	GCGTATCTTGAT	CATGCTGCCTCCCGTAGGAGT	F32Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Forl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left arm	sample126	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M24Nost	GCACTCGTTAGA	CATGCTGCCTCCCGTAGGAGT	M24Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample288	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M11Nose	ACAGTGCTTCAT	CATGCTGCCTCCCGTAGGAGT	M11Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Nose	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:External nose	sample025	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M23Uric	GATGTGAGCGCT	CATGCTGCCTCCCGTAGGAGT	M23Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample583	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M2	M2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M13Fotl	GAAGAGTGATCA	CATGCTGCCTCCCGTAGGAGT	M13Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left foot surface	sample235	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F13Uric	GAGATGCCGACT	CATGCTGCCTCCCGTAGGAGT	F13Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample567	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F1	F1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F12Frhd	AGTCTACTCTGA	CATGCTGCCTCCCGTAGGAGT	F12Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Frhd	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample034	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Mout	ACAGCAGTGGTC	CATGCTGCCTCCCGTAGGAGT	M11Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Mout	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Oral cavity	sample259	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M1	M1	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M13Fotr	GAACTGTATCTC	CATGCTGCCTCCCGTAGGAGT	M13Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right foot surface	sample458	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M13Knee	GAACATGATGAG	CATGCTGCCTCCCGTAGGAGT	M13Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Popliteal fossa	sample007	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F33Knee	GTATGCGCTGTA	CATGCTGCCTCCCGTAGGAGT	F33Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Popliteal fossa	sample005	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F14Nost	GAGTAGCTCGTG	CATGCTGCCTCCCGTAGGAGT	F14Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample280	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M24Fotr	GCAGCACGTTGA	CATGCTGCCTCCCGTAGGAGT	M24Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right foot surface	sample463	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F13Fotr	GACTTCAGTGTG	CATGCTGCCTCCCGTAGGAGT	F13Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample446	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Urin	CTGCAGTACTTA	CATGCTGCCTCCCGTAGGAGT	M32Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Urin	0.006	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample560	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M3	M3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F12Fotr	ATACTCACTCAG	CATGCTGCCTCCCGTAGGAGT	F12Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Fotr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample445	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Plmr	GCAGTATCACTG	CATGCTGCCTCCCGTAGGAGT	F31Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Plmr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample420	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Plml	GCAGGCAGTACT	CATGCTGCCTCCCGTAGGAGT	F31Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Plml	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample197	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Fotl	ATACTATTGCGC	CATGCTGCCTCCCGTAGGAGT	F12Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Fotl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample222	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M44Nost	TAACTCTGATGC	CATGCTGCCTCCCGTAGGAGT	M44Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample292	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M24Fotl	GCAGCCGAGTAT	CATGCTGCCTCCCGTAGGAGT	M24Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left foot surface	sample240	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F13Fotl	GAGAATACGTGA	CATGCTGCCTCCCGTAGGAGT	F13Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample223	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Hair	ACGTCTGTAGCA	CATGCTGCCTCCCGTAGGAGT	M12Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Hair	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Head hair	sample080	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.F11Ewxl	AGACCGTCAGAC	CATGCTGCCTCCCGTAGGAGT	F11Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Ewxl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left external auditory canal	sample176	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F14Ewax	GAGTGGTAGAGA	CATGCTGCCTCCCGTAGGAGT	F14Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External auditory canal	sample298	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F1	F1	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M53Knee	TACTACATGGTC	CATGCTGCCTCCCGTAGGAGT	M53Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Popliteal fossa	sample015	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Aptl	ATATCGCTACTG	CATGCTGCCTCCCGTAGGAGT	F21Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Aptl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left axilla	sample095	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F23Ewax	GCGACTTGTGTA	CATGCTGCCTCCCGTAGGAGT	F23Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:External auditory canal	sample299	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F2	F2	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F33Fcsw	GTCGACTCCTCT	CATGCTGCCTCCCGTAGGAGT	F33Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample492	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F3	F3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M12Fotl	ACTCTTCTAGAG	CATGCTGCCTCCCGTAGGAGT	M12Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Fotl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left foot surface	sample234	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Navl	GCTCGCTACTTC	CATGCTGCCTCCCGTAGGAGT	F32Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Navl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Umbilicus	sample271	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F14Fcsw	GATATGCGGCTG	CATGCTGCCTCCCGTAGGAGT	F14Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample481	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F1	F1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F21Urin	ATGGTCTACTAC	CATGCTGCCTCCCGTAGGAGT	F21Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Urin	0.006	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample555	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F2	F2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M22Pinl	CGATGTCGTCAA	CATGCTGCCTCCCGTAGGAGT	M22Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Pinl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of left pinna	sample171	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F13Plmr	GACTCACTCAAT	CATGCTGCCTCCCGTAGGAGT	F13Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample414	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Kner	AGGCTACACGAC	CATGCTGCCTCCCGTAGGAGT	F12Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Kner	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right popliteal fossa	sample330	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Fotl	GATACGTCCTGA	CATGCTGCCTCCCGTAGGAGT	M42Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Fotl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left foot surface	sample246	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Fotl	GACCGAGCTATG	CATGCTGCCTCCCGTAGGAGT	M41Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Fotl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left foot surface	sample245	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Fotr	ACTGACAGCCAT	CATGCTGCCTCCCGTAGGAGT	M12Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Fotr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right foot surface	sample457	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Fotr	GATAGCTGTCTT	CATGCTGCCTCCCGTAGGAGT	M42Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Fotr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right foot surface	sample469	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Frhd	GCTAAGAGAGTA	CATGCTGCCTCCCGTAGGAGT	F32Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Frhd	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample042	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Knel	AGGACGCACTGT	CATGCTGCCTCCCGTAGGAGT	F12Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Knel	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left popliteal fossa	sample108	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F13Plml	GACTCGAATCGT	CATGCTGCCTCCCGTAGGAGT	F13Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample191	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Tong	CTGAGCAGAGTC	CATGCTGCCTCCCGTAGGAGT	M32Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Tong	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample542	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M3	M3	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F21Mout	ATCTTAGACTGC	CATGCTGCCTCCCGTAGGAGT	F21Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Mout	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Oral cavity	sample255	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F2	F2	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F22Indr	CACAGTGGACGT	CATGCTGCCTCCCGTAGGAGT	F22Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Indr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right index finger	sample360	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Nstr	GCTGGTATCTGA	CATGCTGCCTCCCGTAGGAGT	F32Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Nstr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample376	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M43Knee	GTGGCGATACAC	CATGCTGCCTCCCGTAGGAGT	M43Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Popliteal fossa	sample013	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M14Frhd	GACATCGGCTAT	CATGCTGCCTCCCGTAGGAGT	M14Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Forehead	sample048	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Tong	CGCAGCGGTATA	CATGCTGCCTCCCGTAGGAGT	M22Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Tong	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Dorsal surface of tongue	sample538	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M2	M2	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F13Fcsw	GAGCAGATGCCT	CATGCTGCCTCCCGTAGGAGT	F13Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample480	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F1	F1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F33Plml	GTATATCCGCAG	CATGCTGCCTCCCGTAGGAGT	F33Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample199	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Labi	GCACGACAACAC	CATGCTGCCTCCCGTAGGAGT	F31Labi	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Labi	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Frenulum of labia minora	sample091	False	UBERON:skin	UBERON:mucus	UBERON:labia minora	2008-2009	human skin metagenome	labia minora	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:mucus	Negative	human	F3	F3	9606	40.0149856	-105.2705456	labia minora	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F33Plmr	GTAGTGTCTAGC	CATGCTGCCTCCCGTAGGAGT	F33Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample422	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M44Urin	TACATCACCACA	CATGCTGCCTCCCGTAGGAGT	M44Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample594	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M4	M4	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F32Nstl	GCTGCTGCAATA	CATGCTGCCTCCCGTAGGAGT	F32Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Nstl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample154	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F22Indl	CACAGCTCGAAT	CATGCTGCCTCCCGTAGGAGT	F22Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Indl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left index finger	sample138	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F33Nost	GTATGACTGGCT	CATGCTGCCTCCCGTAGGAGT	F33Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample283	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M42Navl	GAGCATTCTCTA	CATGCTGCCTCCCGTAGGAGT	M42Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Navl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Umbilicus	sample278	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Aptr	ACTGTGACTTCA	CATGCTGCCTCCCGTAGGAGT	F11Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Aptr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right axilla	sample315	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F13Frhd	GACTGATCATCT	CATGCTGCCTCCCGTAGGAGT	F13Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample035	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Aptl	ACTGTCGAAGCT	CATGCTGCCTCCCGTAGGAGT	F11Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Aptl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left axilla	sample093	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Glns	CAGTGCATATGC	CATGCTGCCTCCCGTAGGAGT	M21Glns	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Glns	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Glans penis	sample067	False	UBERON:skin	UBERON:sebum	UBERON:glans penis	2008-2009	human skin metagenome	glans penis	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	glans penis	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Nstr	CACGTGACATGT	CATGCTGCCTCCCGTAGGAGT	F22Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Nstr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample374	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M12Ewxl	ACGCAACTGCTA	CATGCTGCCTCCCGTAGGAGT	M12Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Ewxl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left external auditory canal	sample182	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M12Pinl	ACTCGATTCGAT	CATGCTGCCTCCCGTAGGAGT	M12Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Pinl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of left pinna	sample169	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Aptl	AACGCACGCTAG	CATGCTGCCTCCCGTAGGAGT	M11Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Aptl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left axilla	sample099	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Frhd	GATGTGAGCGCT	CATGCTGCCTCCCGTAGGAGT	F31Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Frhd	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample041	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Pinr	ACTCGCACAGGA	CATGCTGCCTCCCGTAGGAGT	M12Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Pinr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of right pinna	sample392	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Ewxr	ACGCGATACTGG	CATGCTGCCTCCCGTAGGAGT	M12Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Ewxr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right external auditory canal	sample405	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M12Tong	ACTGATCCTAGT	CATGCTGCCTCCCGTAGGAGT	M12Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Tong	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Dorsal surface of tongue	sample534	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M1	M1	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F22Nstl	CACGTCGATGGA	CATGCTGCCTCCCGTAGGAGT	F22Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Nstl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample152	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F31Indl	GCAATAGCTGCT	CATGCTGCCTCCCGTAGGAGT	F31Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Indl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left index finger	sample139	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Pinr	GACCACTACGAT	CATGCTGCCTCCCGTAGGAGT	M41Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Pinr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of right pinna	sample397	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Frhd	CTATGCTTGATG	CATGCTGCCTCCCGTAGGAGT	M32Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Frhd	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample054	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M43Uric	GTTAGAGCACTC	CATGCTGCCTCCCGTAGGAGT	M43Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample591	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M4	M4	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M43Urin	GTGTTGCAGCAT	CATGCTGCCTCCCGTAGGAGT	M43Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample592	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M4	M4	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M21Indl	CATACCAGTAGC	CATGCTGCCTCCCGTAGGAGT	M21Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Indl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left index finger	sample143	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Navl	GAAGTCTCGCAT	CATGCTGCCTCCCGTAGGAGT	M41Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Navl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Umbilicus	sample277	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M23Urin	GATGTCGTGTCA	CATGCTGCCTCCCGTAGGAGT	M23Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample584	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M2	M2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F11Ewxr	AGACGTGCACTG	CATGCTGCCTCCCGTAGGAGT	F11Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Ewxr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right external auditory canal	sample399	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M41Pinl	GACATCGGCTAT	CATGCTGCCTCCCGTAGGAGT	M41Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Pinl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of left pinna	sample174	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M13Frhd	CTTGATGCGTAT	CATGCTGCCTCCCGTAGGAGT	M13Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Forehead	sample047	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Ewxr	CGGCGATGTACA	CATGCTGCCTCCCGTAGGAGT	M31Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Ewxr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right external auditory canal	sample408	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F12Indr	AGTGCGATGCGT	CATGCTGCCTCCCGTAGGAGT	F12Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Indr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right index finger	sample358	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M13Ewax	GAAGCTACTGTC	CATGCTGCCTCCCGTAGGAGT	M13Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:External auditory canal	sample303	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M1	M1	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M41Forl	CTGTTCGTAGAG	CATGCTGCCTCCCGTAGGAGT	M41Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Forl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of left arm	sample133	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Forr	CTTAGCACATCA	CATGCTGCCTCCCGTAGGAGT	M41Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Forr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of right arm	sample355	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Indl	AGTGAGAGAAGC	CATGCTGCCTCCCGTAGGAGT	F12Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Indl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left index finger	sample136	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Frhd	AGAGTCCTGAGC	CATGCTGCCTCCCGTAGGAGT	F11Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Frhd	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample033	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Ewxl	CGGAGTGTCTAT	CATGCTGCCTCCCGTAGGAGT	M31Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Ewxl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left external auditory canal	sample185	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M21Pinr	CATGCAGACTGT	CATGCTGCCTCCCGTAGGAGT	M21Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Pinr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of right pinna	sample393	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M33Fcsw	GGTATACGCAGC	CATGCTGCCTCCCGTAGGAGT	M33Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample510	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M3	M3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M23Tong	GATGCATGACGC	CATGCTGCCTCCCGTAGGAGT	M23Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Dorsal surface of tongue	sample539	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M2	M2	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M41Kner	CTGGCTGTATGA	CATGCTGCCTCCCGTAGGAGT	M41Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Kner	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right popliteal fossa	sample341	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Knel	GATCGCAGGTGT	CATGCTGCCTCCCGTAGGAGT	F31Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Knel	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left popliteal fossa	sample111	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Hair	GAACATGATGAG	CATGCTGCCTCCCGTAGGAGT	M41Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Hair	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Head hair	sample085	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.M41Knel	CTGGAGCATGAC	CATGCTGCCTCCCGTAGGAGT	M41Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Knel	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left popliteal fossa	sample119	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F24Uric	GCTGCTGCAATA	CATGCTGCCTCCCGTAGGAGT	F24Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample573	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F2	F2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M21Hair	CAGTGTCAGGAC	CATGCTGCCTCCCGTAGGAGT	M21Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Hair	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Head hair	sample081	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.F24Urin	GCTGATGAGCTG	CATGCTGCCTCCCGTAGGAGT	F24Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample574	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F2	F2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F22Tong	CAGACTCGCAGA	CATGCTGCCTCCCGTAGGAGT	F22Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Tong	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Dorsal surface of tongue	sample526	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F2	F2	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F31Indr	GCACATCGAGCA	CATGCTGCCTCCCGTAGGAGT	F31Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Indr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right index finger	sample361	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Navl	AGTGTCACGGTG	CATGCTGCCTCCCGTAGGAGT	F12Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Navl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Umbilicus	sample268	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F24Ewax	GCTCAGTGCAGA	CATGCTGCCTCCCGTAGGAGT	F24Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:External auditory canal	sample300	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F2	F2	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F12Fcsw	AGTAGTATCCTC	CATGCTGCCTCCCGTAGGAGT	F12Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Fcsw	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample479	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F1	F1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F33Urin	GTCATTCACGAG	CATGCTGCCTCCCGTAGGAGT	F33Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample576	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F3	F3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F12Fcsp	AGTACTGCAGGC	CATGCTGCCTCCCGTAGGAGT	F12Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Fcsp	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample478	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F1	F1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F33Uric	GTCCATAGCTAG	CATGCTGCCTCCCGTAGGAGT	F33Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample575	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F3	F3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F33Ewax	GTCACGACTATT	CATGCTGCCTCCCGTAGGAGT	F33Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External auditory canal	sample301	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F3	F3	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F12Tong	ATAGCTCCATAC	CATGCTGCCTCCCGTAGGAGT	F12Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Tong	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample522	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F1	F1	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M11Forr	ACACGAGCCACA	CATGCTGCCTCCCGTAGGAGT	M11Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Forr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of right arm	sample349	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Plmr	CACTCAACAGAC	CATGCTGCCTCCCGTAGGAGT	F22Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Plmr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right palm	sample417	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Plml	CACTACTGTTGA	CATGCTGCCTCCCGTAGGAGT	F22Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Plml	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left palm	sample194	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Hair	AGATACACGCGC	CATGCTGCCTCCCGTAGGAGT	F11Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Hair	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Head hair	sample073	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.M34Fotl	GTAGACTGCGTG	CATGCTGCCTCCCGTAGGAGT	M34Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample244	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Indr	CGTCAGACGGAT	CATGCTGCCTCCCGTAGGAGT	M31Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Indr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right index finger	sample367	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Pinr	CACTGGTATATC	CATGCTGCCTCCCGTAGGAGT	F22Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Pinr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of right pinna	sample388	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Fcsp	CTGTGACATTGT	CATGCTGCCTCCCGTAGGAGT	M41Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Fcsp	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample511	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M4	M4	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M41Ewxr	CTGTCTCTCCTA	CATGCTGCCTCCCGTAGGAGT	M41Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Ewxr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right external auditory canal	sample410	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F23Tong	GCGAGATCCAGT	CATGCTGCCTCCCGTAGGAGT	F23Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Dorsal surface of tongue	sample527	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F2	F2	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M22Fotr	CGCAGACAGACT	CATGCTGCCTCCCGTAGGAGT	M22Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Fotr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right foot surface	sample461	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Fotl	CGCACTCTAGAA	CATGCTGCCTCCCGTAGGAGT	M22Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Fotl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left foot surface	sample238	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Pinr	ATGCGTAGTGCG	CATGCTGCCTCCCGTAGGAGT	F21Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Pinr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of right pinna	sample387	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Ewxl	CTGTATCGTATG	CATGCTGCCTCCCGTAGGAGT	M41Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Ewxl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left external auditory canal	sample187	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M13Urin	GAATGATGAGTG	CATGCTGCCTCCCGTAGGAGT	M13Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample580	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M1	M1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M11Ewxl	AAGCTGCAGTCG	CATGCTGCCTCCCGTAGGAGT	M11Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Ewxl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left external auditory canal	sample181	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M42Aptl	GACGCTAGTTCA	CATGCTGCCTCCCGTAGGAGT	M42Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Aptl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left axilla	sample106	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Pinl	CACTCTGATTAG	CATGCTGCCTCCCGTAGGAGT	F22Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Pinl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of left pinna	sample165	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M34Fotr	GTACTCTAGACT	CATGCTGCCTCCCGTAGGAGT	M34Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample467	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M53Plml	TACGGTATGTCT	CATGCTGCCTCCCGTAGGAGT	M53Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Left palm	sample217	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M44Fotl	TACACGATCTAC	CATGCTGCCTCCCGTAGGAGT	M44Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left foot surface	sample248	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M53Frhd	TACGTGTACGTG	CATGCTGCCTCCCGTAGGAGT	M53Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Forehead	sample061	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Frhd	GAGAATACGTGA	CATGCTGCCTCCCGTAGGAGT	M42Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Frhd	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Forehead	sample058	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M44Fotr	TACACACATGGC	CATGCTGCCTCCCGTAGGAGT	M44Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right foot surface	sample471	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M33Frhd	GCTTACATCGAG	CATGCTGCCTCCCGTAGGAGT	M33Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample055	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M53Plmr	TACGCGCTGAGA	CATGCTGCCTCCCGTAGGAGT	M53Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Right palm	sample440	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M14Knee	GACCGAGCTATG	CATGCTGCCTCCCGTAGGAGT	M14Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Popliteal fossa	sample008	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Hair	ATCTACTACACG	CATGCTGCCTCCCGTAGGAGT	F21Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Hair	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Head hair	sample075	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.F23Plml	GCATCGTCAACA	CATGCTGCCTCCCGTAGGAGT	F23Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left palm	sample195	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Nstl	GCAGCCGAGTAT	CATGCTGCCTCCCGTAGGAGT	F31Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Nstl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample153	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M42Aptr	GACGTTGCACAG	CATGCTGCCTCCCGTAGGAGT	M42Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Aptr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right axilla	sample328	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F33Frhd	GTATCCATGCGA	CATGCTGCCTCCCGTAGGAGT	F33Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample043	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Fcsw	CTGTGGATCGAT	CATGCTGCCTCCCGTAGGAGT	M41Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Fcsw	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample512	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M4	M4	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M24Ewax	GCAGGATAGATA	CATGCTGCCTCCCGTAGGAGT	M24Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:External auditory canal	sample306	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M2	M2	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M31Urin	CTACGCGTCTCT	CATGCTGCCTCCCGTAGGAGT	M31Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Urin	0.006	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample559	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M3	M3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M11Tong	ACCGCAGAGTCA	CATGCTGCCTCCCGTAGGAGT	M11Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Tong	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Dorsal surface of tongue	sample533	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M1	M1	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M13Plmr	CTGTTCGTAGAG	CATGCTGCCTCCCGTAGGAGT	M13Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right palm	sample426	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F23Nost	GCATTGCGTGAG	CATGCTGCCTCCCGTAGGAGT	F23Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample281	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F21Plmr	ATGCAGCTCAGT	CATGCTGCCTCCCGTAGGAGT	F21Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Plmr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right palm	sample416	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F23Plmr	GCATATAGTCTC	CATGCTGCCTCCCGTAGGAGT	F23Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right palm	sample418	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Fotl	CTGACACGACAG	CATGCTGCCTCCCGTAGGAGT	M32Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Fotl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample242	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M14Ewax	GACGCAGTAGCT	CATGCTGCCTCCCGTAGGAGT	M14Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:External auditory canal	sample304	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M1	M1	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F24Tong	GCTCGCTACTTC	CATGCTGCCTCCCGTAGGAGT	F24Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Dorsal surface of tongue	sample528	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F2	F2	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M13Plml	CTTAGCACATCA	CATGCTGCCTCCCGTAGGAGT	M13Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left palm	sample203	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Tong	GCATGTGCATGT	CATGCTGCCTCCCGTAGGAGT	F31Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Tong	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample529	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F3	F3	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M32Glns	CTCAATGACTCA	CATGCTGCCTCCCGTAGGAGT	M32Glns	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Glns	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Glans penis	sample070	False	UBERON:skin	UBERON:sebum	UBERON:glans penis	2008-2009	human skin metagenome	glans penis	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	glans penis	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Nstl	AGTTCAGACGCT	CATGCTGCCTCCCGTAGGAGT	F12Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Nstl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample150	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F12Mout	AGTGGATGCTCT	CATGCTGCCTCCCGTAGGAGT	F12Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Mout	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Oral cavity	sample254	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F1	F1	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M33Fotl	GGATCGCAGATC	CATGCTGCCTCCCGTAGGAGT	M33Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample243	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Frhd	CAAGTGAGAGAG	CATGCTGCCTCCCGTAGGAGT	F22Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Frhd	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Forehead	sample038	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Pinr	CGCACATGTTAT	CATGCTGCCTCCCGTAGGAGT	M22Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Pinr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of right pinna	sample394	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M54Knee	TAGCGACATCTG	CATGCTGCCTCCCGTAGGAGT	M54Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Popliteal fossa	sample016	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Nstr	AGTTCTACGTCA	CATGCTGCCTCCCGTAGGAGT	F12Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Nstr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample372	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M21Fcsp	CAGGTGCTACTA	CATGCTGCCTCCCGTAGGAGT	M21Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Fcsp	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample500	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M2	M2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M21Fcsw	CAGTACGATCTT	CATGCTGCCTCCCGTAGGAGT	M21Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Fcsw	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample501	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M2	M2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M54Tong	TAGGTATCTCAC	CATGCTGCCTCCCGTAGGAGT	M54Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Dorsal surface of tongue	sample550	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M5	M5	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F21Tong	ATGGCGTGCACA	CATGCTGCCTCCCGTAGGAGT	F21Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Tong	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Dorsal surface of tongue	sample525	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F2	F2	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F11Fotl	AGCGTAGGTCGT	CATGCTGCCTCCCGTAGGAGT	F11Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Fotl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample221	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Knel	CGCTAGAACGCA	CATGCTGCCTCCCGTAGGAGT	M31Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Knel	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left popliteal fossa	sample117	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Ewxl	GACTCACTCAAT	CATGCTGCCTCCCGTAGGAGT	M42Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Ewxl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left external auditory canal	sample188	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M31Navl	CGTGACAATGTC	CATGCTGCCTCCCGTAGGAGT	M31Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Navl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Umbilicus	sample276	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F13Tong	GAGAGAATGATC	CATGCTGCCTCCCGTAGGAGT	F13Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample523	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F1	F1	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M24Uric	GCAGTTCATATC	CATGCTGCCTCCCGTAGGAGT	M24Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample585	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M2	M2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M42Ewxr	GACTCGAATCGT	CATGCTGCCTCCCGTAGGAGT	M42Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Ewxr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right external auditory canal	sample411	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M31Kner	CGCTTATCGAGA	CATGCTGCCTCCCGTAGGAGT	M31Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Kner	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right popliteal fossa	sample339	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M13Uric	GACACTCGAATC	CATGCTGCCTCCCGTAGGAGT	M13Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample579	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M1	M1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F13Nost	GACTGCATCTTA	CATGCTGCCTCCCGTAGGAGT	F13Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample279	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F11Fotr	AGCTATCCACGA	CATGCTGCCTCCCGTAGGAGT	F11Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Fotr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample444	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Forl	CAGTCACTAACG	CATGCTGCCTCCCGTAGGAGT	M21Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Forl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of left arm	sample129	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M24Urin	GCAGTATCACTG	CATGCTGCCTCCCGTAGGAGT	M24Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample586	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M2	M2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F32Hair	GCTAGATGCCAG	CATGCTGCCTCCCGTAGGAGT	F32Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Hair	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Head hair	sample078	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.F32Mout	GCTCAGTGCAGA	CATGCTGCCTCCCGTAGGAGT	F32Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Mout	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Oral cavity	sample258	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F3	F3	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F31Pinr	GCATAGTAGCCG	CATGCTGCCTCCCGTAGGAGT	F31Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Pinr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right pinna	sample389	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Indl	CTCATGTACAGT	CATGCTGCCTCCCGTAGGAGT	M32Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Indl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left index finger	sample146	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Pinl	GCTTACATCGAG	CATGCTGCCTCCCGTAGGAGT	F32Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Pinl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left pinna	sample167	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M64Frhd	TCACTGGCAGTA	CATGCTGCCTCCCGTAGGAGT	M64Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Forehead	sample064	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Pinr	GCTTCATAGTGT	CATGCTGCCTCCCGTAGGAGT	F32Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Pinr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right pinna	sample390	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Indr	CTCCACATGAGA	CATGCTGCCTCCCGTAGGAGT	M32Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Indr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right index finger	sample368	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Pinl	GCAGTTCATATC	CATGCTGCCTCCCGTAGGAGT	F31Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Pinl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left pinna	sample166	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Hair	GATTAGCACTCT	CATGCTGCCTCCCGTAGGAGT	F31Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Hair	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Head hair	sample077	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.M31Indl	CGTCACGACTAA	CATGCTGCCTCCCGTAGGAGT	M31Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Indl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left index finger	sample145	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Fotl	GCTTGCGAGACA	CATGCTGCCTCCCGTAGGAGT	F32Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Fotl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample230	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M53Nost	TACTAATCTGCG	CATGCTGCCTCCCGTAGGAGT	M53Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Nares	sample293	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F11Nstr	AGCATATGAGAG	CATGCTGCCTCCCGTAGGAGT	F11Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Nstr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample371	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F11Nstl	AGCAGTCGCGAT	CATGCTGCCTCCCGTAGGAGT	F11Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Nstl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample149	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F32Fotr	GGACGTCACAGT	CATGCTGCCTCCCGTAGGAGT	F32Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Fotr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample453	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F14Knee	GAGTATGCAGCC	CATGCTGCCTCCCGTAGGAGT	F14Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Popliteal fossa	sample002	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M34Frhd	GGTGCGTGTATG	CATGCTGCCTCCCGTAGGAGT	M34Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample056	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Forr	ACGGATCGTCAG	CATGCTGCCTCCCGTAGGAGT	M12Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Forr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of right arm	sample350	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M53Fotr	TACTGCGACAGT	CATGCTGCCTCCCGTAGGAGT	M53Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Right foot surface	sample472	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Aptr	CCAGATGATCGT	CATGCTGCCTCCCGTAGGAGT	M22Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Aptr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right axilla	sample324	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Aptr	ATATGCCAGTGC	CATGCTGCCTCCCGTAGGAGT	F21Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Aptr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right axilla	sample317	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F14Uric	GATAGTGCCACT	CATGCTGCCTCCCGTAGGAGT	F14Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample569	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F1	F1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F13Urin	GAGAGCTCTACG	CATGCTGCCTCCCGTAGGAGT	F13Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample568	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F1	F1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F11Nose	AGCAGCACTTGT	CATGCTGCCTCCCGTAGGAGT	F11Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Nose	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External nose	sample019	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Nose	AGTGTTCGATCG	CATGCTGCCTCCCGTAGGAGT	F12Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Nose	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External nose	sample020	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M33Nost	GCTTCATAGTGT	CATGCTGCCTCCCGTAGGAGT	M33Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample289	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M22Aptl	CATTGTCTGTGA	CATGCTGCCTCCCGTAGGAGT	M22Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Aptl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left axilla	sample102	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M53Fotl	TACTGGACGCGA	CATGCTGCCTCCCGTAGGAGT	M53Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Left foot surface	sample249	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F14Urin	GATAGCTGTCTT	CATGCTGCCTCCCGTAGGAGT	F14Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample570	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F1	F1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M12Forl	ACGCTCATGGAT	CATGCTGCCTCCCGTAGGAGT	M12Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Forl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of left arm	sample128	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Forl	AGTCACATCACT	CATGCTGCCTCCCGTAGGAGT	F12Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Forl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left arm	sample122	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M44Fcsw	TACGATGACCAC	CATGCTGCCTCCCGTAGGAGT	M44Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample516	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M4	M4	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M31Frhd	CGTATCTGCGAA	CATGCTGCCTCCCGTAGGAGT	M31Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Frhd	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample053	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Forr	AGTCCATAGCTG	CATGCTGCCTCCCGTAGGAGT	F12Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Forr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right arm	sample344	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F23Fcsw	GCGTACAACTGT	CATGCTGCCTCCCGTAGGAGT	F23Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample486	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F2	F2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F21Nstr	TCATCGCGATAT	CATGCTGCCTCCCGTAGGAGT	F21Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Nstr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample373	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F13Knee	GACTGTCATGCA	CATGCTGCCTCCCGTAGGAGT	F13Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F13Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Popliteal fossa	sample001	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M54Nost	TAGCCTCTCTGC	CATGCTGCCTCCCGTAGGAGT	M54Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Nares	sample294	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M23Fotr	GATCTCATAGGC	CATGCTGCCTCCCGTAGGAGT	M23Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right foot surface	sample462	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Hair	AGTCTCGCATAT	CATGCTGCCTCCCGTAGGAGT	F12Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Hair	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Head hair	sample074	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.M23Fotl	GATCTTCAGTAC	CATGCTGCCTCCCGTAGGAGT	M23Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left foot surface	sample239	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Nstl	ATGAGACTCCAC	CATGCTGCCTCCCGTAGGAGT	F21Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Nstl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample151	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M54Fcsw	TAGTGTGCTTCA	CATGCTGCCTCCCGTAGGAGT	M54Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Feces	sample518	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M5	M5	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F32Tong	GGATCGCAGATC	CATGCTGCCTCCCGTAGGAGT	F32Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Tong	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample530	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F3	F3	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M11Fotr	ACCAGCGACTAG	CATGCTGCCTCCCGTAGGAGT	M11Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Fotr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right foot surface	sample456	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Navl	CATATACTCGCA	CATGCTGCCTCCCGTAGGAGT	M21Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Navl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Umbilicus	sample274	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Knel	CCAGTGTATGCA	CATGCTGCCTCCCGTAGGAGT	M22Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Knel	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left popliteal fossa	sample116	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M44Knee	TAAGCGCAGCAC	CATGCTGCCTCCCGTAGGAGT	M44Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Popliteal fossa	sample014	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Kner	CCATACATAGCT	CATGCTGCCTCCCGTAGGAGT	M22Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Kner	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right popliteal fossa	sample338	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Fotl	ACCAGACGATGC	CATGCTGCCTCCCGTAGGAGT	M11Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Fotl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left foot surface	sample233	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Urin	GATATGCGGCTG	CATGCTGCCTCCCGTAGGAGT	M42Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Urin	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample566	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M4	M4	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M63Nost	TATCGCGCGATA	CATGCTGCCTCCCGTAGGAGT	M63Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Nares	sample295	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M42Forr	GACTTCAGTGTG	CATGCTGCCTCCCGTAGGAGT	M42Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Forr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of right arm	sample356	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Fcsw	GACTGCATCTTA	CATGCTGCCTCCCGTAGGAGT	M42Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Fcsw	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample514	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M4	M4	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F21Ewxr	ATCCGATCACAG	CATGCTGCCTCCCGTAGGAGT	F21Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Ewxr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right external auditory canal	sample401	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M42Fcsp	GACTGATCATCT	CATGCTGCCTCCCGTAGGAGT	M42Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Fcsp	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample513	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M4	M4	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M12Plml	ACTCACGGTATG	CATGCTGCCTCCCGTAGGAGT	M12Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Plml	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left palm	sample202	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Tong	GATAGTGCCACT	CATGCTGCCTCCCGTAGGAGT	M42Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Tong	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Dorsal surface of tongue	sample546	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M4	M4	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M42Forl	GACTGTCATGCA	CATGCTGCCTCCCGTAGGAGT	M42Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Forl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of left arm	sample134	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Hair	CGTCAACGATGT	CATGCTGCCTCCCGTAGGAGT	M31Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Hair	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Head hair	sample083	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.F23Uric	GCGGATGTGACT	CATGCTGCCTCCCGTAGGAGT	F23Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample571	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F2	F2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F21Forr	ATCGCTCGAGGA	CATGCTGCCTCCCGTAGGAGT	F21Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Forr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of right arm	sample345	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Hair	CGACTTATGTGT	CATGCTGCCTCCCGTAGGAGT	M22Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Hair	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Head hair	sample082	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.M42Hair	GAGAGAATGATC	CATGCTGCCTCCCGTAGGAGT	M42Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Hair	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Head hair	sample086	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.F14Plmr	GAGCATTCTCTA	CATGCTGCCTCCCGTAGGAGT	F14Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample415	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F23Urin	GCGATATATCGC	CATGCTGCCTCCCGTAGGAGT	F23Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample572	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F2	F2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F14Plml	GAGCTGGCTGAT	CATGCTGCCTCCCGTAGGAGT	F14Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample192	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Forl	ATCGCGGACGAT	CATGCTGCCTCCCGTAGGAGT	F21Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Forl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of left arm	sample123	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Ewxl	GCGAGATCCAGT	CATGCTGCCTCCCGTAGGAGT	F32Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Ewxl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left external auditory canal	sample180	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F32Aptr	GCCAGAGTCGTA	CATGCTGCCTCCCGTAGGAGT	F32Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Aptr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right axilla	sample320	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Frhd	ACGGTGAGTGTC	CATGCTGCCTCCCGTAGGAGT	M12Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Frhd	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Forehead	sample046	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Aptl	GCCACTGATAGT	CATGCTGCCTCCCGTAGGAGT	F32Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Aptl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left axilla	sample098	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Ewxr	GCGATATATCGC	CATGCTGCCTCCCGTAGGAGT	F32Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Ewxr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right external auditory canal	sample404	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M34Urin	GTAGCAACGTCT	CATGCTGCCTCCCGTAGGAGT	M34Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample590	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M3	M3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M24Knee	GCACTGAGACGT	CATGCTGCCTCCCGTAGGAGT	M24Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Popliteal fossa	sample010	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M34Uric	GTAGCGCGAGTT	CATGCTGCCTCCCGTAGGAGT	M34Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample589	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M3	M3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M54Plml	TAGCACACCTAT	CATGCTGCCTCCCGTAGGAGT	M54Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Left palm	sample218	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Glns	CTTGTGTCGATA	CATGCTGCCTCCCGTAGGAGT	M41Glns	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Glns	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Glans penis	sample071	False	UBERON:skin	UBERON:sebum	UBERON:glans penis	2008-2009	human skin metagenome	glans penis	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	glans penis	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Knel	AACTGTGCGTAC	CATGCTGCCTCCCGTAGGAGT	M11Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Knel	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left popliteal fossa	sample113	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Plmr	ACTCAGATACTC	CATGCTGCCTCCCGTAGGAGT	M12Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Plmr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right palm	sample425	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Pinl	ACATTCAGCGCA	CATGCTGCCTCCCGTAGGAGT	M11Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Pinl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of left pinna	sample168	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Nstr	CGTGTACATCAG	CATGCTGCCTCCCGTAGGAGT	M31Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Nstr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample381	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F34Frhd	GTCGTGTGTCAA	CATGCTGCCTCCCGTAGGAGT	F34Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample044	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Nose	GCTGATGAGCTG	CATGCTGCCTCCCGTAGGAGT	F32Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Nose	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External nose	sample024	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Nstl	CGTGCATTATCA	CATGCTGCCTCCCGTAGGAGT	M31Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Nstl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample159	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F23Frhd	GCATGTGCATGT	CATGCTGCCTCCCGTAGGAGT	F23Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Forehead	sample039	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Pinr	ACCACATACATC	CATGCTGCCTCCCGTAGGAGT	M11Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Pinr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of right pinna	sample391	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M13Fcsw	GACAGCGTTGAC	CATGCTGCCTCCCGTAGGAGT	M13Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample498	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M1	M1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F11Mout	AGCACACCTACA	CATGCTGCCTCCCGTAGGAGT	F11Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Mout	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Oral cavity	sample253	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F1	F1	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M54Urin	TAGTCGTCTAGT	CATGCTGCCTCCCGTAGGAGT	M54Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Urine	sample598	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M5	M5	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M21Frhd	CAGTGATCCTAG	CATGCTGCCTCCCGTAGGAGT	M21Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Frhd	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Forehead	sample049	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Knel	ACTTGTAGCAGC	CATGCTGCCTCCCGTAGGAGT	F11Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Knel	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left popliteal fossa	sample107	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M54Uric	TAGTGCTGCGTA	CATGCTGCCTCCCGTAGGAGT	M54Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Urine	sample597	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M5	M5	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F34Fotl	GTCTCTCTACGC	CATGCTGCCTCCCGTAGGAGT	F34Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample232	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Fcsw	GATGATCGCCGA	CATGCTGCCTCCCGTAGGAGT	F31Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Fcsw	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample489	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F3	F3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F31Fcsp	GATCTTCAGTAC	CATGCTGCCTCCCGTAGGAGT	F31Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Fcsp	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample488	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F3	F3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F12Labi	AGTTAGTGCGTC	CATGCTGCCTCCCGTAGGAGT	F12Labi	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Labi	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Frenulum of labia minora	sample088	False	UBERON:skin	UBERON:mucus	UBERON:labia minora	2008-2009	human skin metagenome	labia minora	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:mucus	Negative	human	F1	F1	9606	40.0149856	-105.2705456	labia minora	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M34Ewax	GTAGAGCTGTTC	CATGCTGCCTCCCGTAGGAGT	M34Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External auditory canal	sample308	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M3	M3	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M44Plmr	GTTGACGACAGC	CATGCTGCCTCCCGTAGGAGT	M44Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right palm	sample439	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M43Plml	GTGATAGTGCCG	CATGCTGCCTCCCGTAGGAGT	M43Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left palm	sample215	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Forr	AGAGTAGCTAAG	CATGCTGCCTCCCGTAGGAGT	F11Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Forr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right arm	sample343	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M33Knee	GCTTGCGAGACA	CATGCTGCCTCCCGTAGGAGT	M33Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M33Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Popliteal fossa	sample011	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Plmr	GAGTCTGAGTCT	CATGCTGCCTCCCGTAGGAGT	M42Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Plmr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right palm	sample437	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Plml	GAGTATGCAGCC	CATGCTGCCTCCCGTAGGAGT	M42Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Plml	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left palm	sample214	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F32Fcsw	GCGTACAACTGT	CATGCTGCCTCCCGTAGGAGT	F32Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Fcsw	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample491	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F3	F3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F32Fcsp	GCGGATGTGACT	CATGCTGCCTCCCGTAGGAGT	F32Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Fcsp	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample490	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F3	F3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F11Forl	AGAGCAAGAGCA	CATGCTGCCTCCCGTAGGAGT	F11Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Forl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left arm	sample121	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M63Frhd	TATCAGGTGTGC	CATGCTGCCTCCCGTAGGAGT	M63Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Forehead	sample063	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M44Plml	GTTGTATACTCG	CATGCTGCCTCCCGTAGGAGT	M44Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left palm	sample216	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M43Plmr	GTGAGGTCGCTA	CATGCTGCCTCCCGTAGGAGT	M43Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right palm	sample438	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Ewxr	GATCTCATAGGC	CATGCTGCCTCCCGTAGGAGT	F31Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Ewxr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right external auditory canal	sample403	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F33Tong	GTCATATCGTAC	CATGCTGCCTCCCGTAGGAGT	F33Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F33Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample531	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F3	F3	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M53Fcsw	TAGATAGCAGGA	CATGCTGCCTCCCGTAGGAGT	M53Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Feces	sample517	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M5	M5	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F24Fotl	GCTATTCGACAT	CATGCTGCCTCCCGTAGGAGT	F24Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left foot surface	sample228	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M64Fotl	TCAGCCATGACA	CATGCTGCCTCCCGTAGGAGT	M64Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Left foot surface	sample252	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Mout	GCACTCGTTAGA	CATGCTGCCTCCCGTAGGAGT	F31Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Mout	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Oral cavity	sample257	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F3	F3	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F34Knee	GTCTATCGGAGT	CATGCTGCCTCCCGTAGGAGT	F34Knee	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Knee	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Popliteal fossa	sample006	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	popliteal fossae	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M64Fotr	TCAGATCCGATG	CATGCTGCCTCCCGTAGGAGT	M64Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Right foot surface	sample475	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Navl	CACGACAGGCTA	CATGCTGCCTCCCGTAGGAGT	F22Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Navl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Umbilicus	sample270	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Fcsw	CAACTATCAGCT	CATGCTGCCTCCCGTAGGAGT	F22Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Fcsw	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample485	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F2	F2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F24Fotr	GCTATCACGAGT	CATGCTGCCTCCCGTAGGAGT	F24Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right foot surface	sample451	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Fcsp	CAACACGCACGA	CATGCTGCCTCCCGTAGGAGT	F22Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Fcsp	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample484	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F2	F2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M12Glns	ACGTACTCAGTG	CATGCTGCCTCCCGTAGGAGT	M12Glns	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Glns	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Glans penis	sample066	False	UBERON:skin	UBERON:sebum	UBERON:glans penis	2008-2009	human skin metagenome	glans penis	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	glans penis	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Indr	AGATCTCTGCAT	CATGCTGCCTCCCGTAGGAGT	F11Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Indr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right index finger	sample357	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M43Tong	GTGTGTGTCAGG	CATGCTGCCTCCCGTAGGAGT	M43Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Dorsal surface of tongue	sample547	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M4	M4	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F31Kner	GATCGTCCAGAT	CATGCTGCCTCCCGTAGGAGT	F31Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Kner	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right popliteal fossa	sample333	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Plmr	CTCTGAAGTCTA	CATGCTGCCTCCCGTAGGAGT	M32Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Plmr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample433	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M43Nost	GTGCACATTATC	CATGCTGCCTCCCGTAGGAGT	M43Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample291	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M21Indr	CATAGACGTTCG	CATGCTGCCTCCCGTAGGAGT	M21Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Indr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right index finger	sample365	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M44Tong	TACAGTCTCATG	CATGCTGCCTCCCGTAGGAGT	M44Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Dorsal surface of tongue	sample548	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M4	M4	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F21Labi	ATCTGGTGCTAT	CATGCTGCCTCCCGTAGGAGT	F21Labi	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Labi	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Frenulum of labia minora	sample089	False	UBERON:skin	UBERON:mucus	UBERON:labia minora	2008-2009	human skin metagenome	labia minora	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:mucus	Negative	human	F2	F2	9606	40.0149856	-105.2705456	labia minora	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Kner	ATCACTAGTCAC	CATGCTGCCTCCCGTAGGAGT	F21Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Kner	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right popliteal fossa	sample331	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Fotr	GCATCGTCAACA	CATGCTGCCTCCCGTAGGAGT	F31Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Fotr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample452	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Fotl	GCATATAGTCTC	CATGCTGCCTCCCGTAGGAGT	F31Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Fotl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left foot surface	sample229	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Knel	ATCACGTAGCGG	CATGCTGCCTCCCGTAGGAGT	F21Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Knel	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left popliteal fossa	sample109	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Indl	GAACTGTATCTC	CATGCTGCCTCCCGTAGGAGT	M41Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Indl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left index finger	sample147	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Knel	GACTAACGTCAC	CATGCTGCCTCCCGTAGGAGT	M42Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Knel	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left popliteal fossa	sample120	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M23Frhd	GATCGCAGGTGT	CATGCTGCCTCCCGTAGGAGT	M23Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Forehead	sample051	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M63Plmr	TAGTTGCGAGTC	CATGCTGCCTCCCGTAGGAGT	M63Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Right palm	sample442	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Nstr	CGATATTCATCG	CATGCTGCCTCCCGTAGGAGT	M22Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Nstr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample380	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M31Glns	CGTATGCTGTAT	CATGCTGCCTCCCGTAGGAGT	M31Glns	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Glns	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Glans penis	sample069	False	UBERON:skin	UBERON:sebum	UBERON:glans penis	2008-2009	human skin metagenome	glans penis	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	glans penis	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F23Fotl	GCCTATACTACA	CATGCTGCCTCCCGTAGGAGT	F23Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left foot surface	sample227	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F23Fotr	GCCAGAGTCGTA	CATGCTGCCTCCCGTAGGAGT	F23Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F23Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right foot surface	sample450	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M44Uric	TACCGCTAGTAG	CATGCTGCCTCCCGTAGGAGT	M44Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample593	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M4	M4	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M22Nstl	CGATAGATCTTC	CATGCTGCCTCCCGTAGGAGT	M22Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Nstl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample158	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M63Plml	TATACGCGCATT	CATGCTGCCTCCCGTAGGAGT	M63Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Left palm	sample219	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Kner	GACTAGACCAGC	CATGCTGCCTCCCGTAGGAGT	M42Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Kner	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right popliteal fossa	sample342	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Indr	GAAGAGTGATCA	CATGCTGCCTCCCGTAGGAGT	M41Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Indr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right index finger	sample369	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Fotr	CAGACATTGCGT	CATGCTGCCTCCCGTAGGAGT	F22Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Fotr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right foot surface	sample449	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M54Frhd	TAGCATCGTGGT	CATGCTGCCTCCCGTAGGAGT	M54Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Forehead	sample062	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Fotr	CTGAGATACGCG	CATGCTGCCTCCCGTAGGAGT	M32Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Fotr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right foot surface	sample465	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Fcsw	AGAGAGCAAGTG	CATGCTGCCTCCCGTAGGAGT	F11Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Fcsw	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample477	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F1	F1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F11Fcsp	AGACTGCGTACT	CATGCTGCCTCCCGTAGGAGT	F11Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Fcsp	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample476	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F1	F1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F21Plml	ATGCACTGGCGA	CATGCTGCCTCCCGTAGGAGT	F21Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Plml	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left palm	sample193	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Fotl	CACTGTAGGACG	CATGCTGCCTCCCGTAGGAGT	F22Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Fotl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left foot surface	sample226	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F34Plml	GTCGTAGCCAGA	CATGCTGCCTCCCGTAGGAGT	F34Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample200	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Aptl	GATCAGAAGATG	CATGCTGCCTCCCGTAGGAGT	F31Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Aptl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left axilla	sample097	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Fcsp	CCTAGTACTGAT	CATGCTGCCTCCCGTAGGAGT	M22Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Fcsp	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample502	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M2	M2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F12Plml	ATAATCTCGTCG	CATGCTGCCTCCCGTAGGAGT	F12Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Plml	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample190	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M44Ewax	TACAGATGGCTC	CATGCTGCCTCCCGTAGGAGT	M44Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:External auditory canal	sample310	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M4	M4	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M64Plmr	TCACGATTAGCG	CATGCTGCCTCCCGTAGGAGT	M64Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Right palm	sample443	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Plmr	ATACACGTGGCG	CATGCTGCCTCCCGTAGGAGT	F12Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Plmr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample413	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Aptr	GATCCGACACTA	CATGCTGCCTCCCGTAGGAGT	F31Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Aptr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right axilla	sample319	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Urin	CGCATGAGGATC	CATGCTGCCTCCCGTAGGAGT	M22Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Urin	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample564	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M2	M2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F22Hair	CACACGTGAGCA	CATGCTGCCTCCCGTAGGAGT	F22Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Hair	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Head hair	sample076	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.M43Fcsw	GTTCGCGTATAG	CATGCTGCCTCCCGTAGGAGT	M43Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Feces	sample515	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M4	M4	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M22Fcsw	CCTCTCGTGATC	CATGCTGCCTCCCGTAGGAGT	M22Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Fcsw	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample503	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M2	M2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M21Aptr	CAGATCGGATCG	CATGCTGCCTCCCGTAGGAGT	M21Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Aptr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right axilla	sample323	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Pinr	GAGTGGTAGAGA	CATGCTGCCTCCCGTAGGAGT	M42Pinr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Pinr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of right pinna	sample398	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	right outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Plml	CGATCGAGTGTT	CATGCTGCCTCCCGTAGGAGT	M22Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Plml	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left palm	sample206	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Fotl	CATGGCTACACA	CATGCTGCCTCCCGTAGGAGT	M21Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Fotl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left foot surface	sample237	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Plmr	CGATGCACCAGA	CATGCTGCCTCCCGTAGGAGT	M22Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Plmr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right palm	sample429	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Fotr	CATGTAATGCTC	CATGCTGCCTCCCGTAGGAGT	M21Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Fotr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right foot surface	sample460	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Pinl	GAGTGAGTACAA	CATGCTGCCTCCCGTAGGAGT	M42Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Pinl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Surface of left pinna	sample175	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Aptl	CAGATACACTTC	CATGCTGCCTCCCGTAGGAGT	M21Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Aptl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left axilla	sample101	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F34Ewax	GTCTGACAGTTG	CATGCTGCCTCCCGTAGGAGT	F34Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External auditory canal	sample302	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F3	F3	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M21Ewxr	CAGCTAGAACGC	CATGCTGCCTCCCGTAGGAGT	M21Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Ewxr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right external auditory canal	sample406	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M63Uric	TCAATCTAGCGT	CATGCTGCCTCCCGTAGGAGT	M63Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Urine	sample599	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M6	M6	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M22Ewxr	CCGATGTCAGAT	CATGCTGCCTCCCGTAGGAGT	M22Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Ewxr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right external auditory canal	sample407	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M43Ewax	GTGTGCTATCAG	CATGCTGCCTCCCGTAGGAGT	M43Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:External auditory canal	sample309	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M4	M4	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M63Urin	TCAACAGCATCG	CATGCTGCCTCCCGTAGGAGT	M63Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Urine	sample600	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M6	M6	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F34Fcsw	GTGACTGCGGAT	CATGCTGCCTCCCGTAGGAGT	F34Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Feces	sample493	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	F3	F3	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	female	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M53Tong	TACTTCGCTCGC	CATGCTGCCTCCCGTAGGAGT	M53Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Dorsal surface of tongue	sample549	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M5	M5	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F34Tong	GTCTGGATAGCG	CATGCTGCCTCCCGTAGGAGT	F34Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample532	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F3	F3	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M34Plmr	GGTCACTGACAG	CATGCTGCCTCCCGTAGGAGT	M34Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample435	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Nose	CTCGATTAGATC	CATGCTGCCTCCCGTAGGAGT	M32Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Nose	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External nose	sample030	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F34Nost	GTCTACACACAT	CATGCTGCCTCCCGTAGGAGT	F34Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample284	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F14Frhd	GAGGCTCATCAT	CATGCTGCCTCCCGTAGGAGT	F14Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Forehead	sample036	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Nose	CGTGATCTCTCC	CATGCTGCCTCCCGTAGGAGT	M31Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Nose	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External nose	sample029	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M64Tong	TCAGGACTGTGT	CATGCTGCCTCCCGTAGGAGT	M64Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Dorsal surface of tongue	sample552	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M6	M6	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M34Plml	GGTCGTAGCGTA	CATGCTGCCTCCCGTAGGAGT	M34Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left palm	sample212	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Forr	CGAATCGACACT	CATGCTGCCTCCCGTAGGAGT	M22Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Forr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of right arm	sample352	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Nstl	GACACTCGAATC	CATGCTGCCTCCCGTAGGAGT	M41Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Nstl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample161	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F12Pinl	ATACAGAGCTCC	CATGCTGCCTCCCGTAGGAGT	F12Pinl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Pinl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of left pinna	sample164	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of outer ear	2008-2009	human skin metagenome	left outer ear	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left lateral pinna	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M53Ewax	TACTTACTGCAG	CATGCTGCCTCCCGTAGGAGT	M53Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:External auditory canal	sample311	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M5	M5	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F14Tong	GATACGTCCTGA	CATGCTGCCTCCCGTAGGAGT	F14Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F14Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample524	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F1	F1	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M22Forl	CGAAGACTGCTG	CATGCTGCCTCCCGTAGGAGT	M22Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Forl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of left arm	sample130	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Nstr	GACAGCGTTGAC	CATGCTGCCTCCCGTAGGAGT	M41Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Nstr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample383	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M42Indr	GAGATGCCGACT	CATGCTGCCTCCCGTAGGAGT	M42Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Indr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right index finger	sample370	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Mout	ACGTTAGCACAC	CATGCTGCCTCCCGTAGGAGT	M12Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Mout	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Oral cavity	sample260	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M1	M1	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M41Frhd	CTTGATGCGTAT	CATGCTGCCTCCCGTAGGAGT	M41Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Frhd	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Forehead	sample057	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F12Ewxr	AGTACGCTCGAG	CATGCTGCCTCCCGTAGGAGT	F12Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Ewxr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right external auditory canal	sample400	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F1	F1	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F22Mout	CACATTGTGAGC	CATGCTGCCTCCCGTAGGAGT	F22Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Mout	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Oral cavity	sample256	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F2	F2	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F12Ewxl	AGGTGTGATCGC	CATGCTGCCTCCCGTAGGAGT	F12Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F12Ewxl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left external auditory canal	sample177	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M24Tong	GCAGGCAGTACT	CATGCTGCCTCCCGTAGGAGT	M24Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Dorsal surface of tongue	sample540	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M2	M2	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M11Hair	ACACTGTTCATG	CATGCTGCCTCCCGTAGGAGT	M11Hair	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Hair	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Head hair	sample079	False	UBERON:hair	UBERON:hair	UBERON:hair	2008-2009	human hair metagenome	hair on head	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	hair on head	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human hair metagenome
449.M21Kner	CAGCATGTGTTG	CATGCTGCCTCCCGTAGGAGT	M21Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Kner	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right popliteal fossa	sample337	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Tong	GACGATATCGCG	CATGCTGCCTCCCGTAGGAGT	M41Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Tong	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Dorsal surface of tongue	sample545	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M4	M4	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F22Kner	ATGTGTCGACTT	CATGCTGCCTCCCGTAGGAGT	F22Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Kner	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right popliteal fossa	sample332	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Kner	AAGAGATGTCGA	CATGCTGCCTCCCGTAGGAGT	M11Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Kner	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right popliteal fossa	sample335	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Knel	ATGTGCACGACT	CATGCTGCCTCCCGTAGGAGT	F22Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Knel	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left popliteal fossa	sample110	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Nose	ACTACGTGTGGT	CATGCTGCCTCCCGTAGGAGT	M12Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Nose	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:External nose	sample026	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M21Knel	CAGCACTAAGCG	CATGCTGCCTCCCGTAGGAGT	M21Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Knel	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left popliteal fossa	sample115	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Nstr	ACTATTGTCACG	CATGCTGCCTCCCGTAGGAGT	M12Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Nstr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample378	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M11Forl	ACACATGTCTAC	CATGCTGCCTCCCGTAGGAGT	M11Forl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Forl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of left arm	sample127	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	left forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M54Fotl	TAGCTCGTAACT	CATGCTGCCTCCCGTAGGAGT	M54Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Left foot surface	sample250	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M54Fotr	TAGCGGATCACG	CATGCTGCCTCCCGTAGGAGT	M54Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Right foot surface	sample473	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Nose	GCAGCACGTTGA	CATGCTGCCTCCCGTAGGAGT	F31Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Nose	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:External nose	sample023	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M54Plmr	TAGATCCTCGAT	CATGCTGCCTCCCGTAGGAGT	M54Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M54Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Right palm	sample441	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M5	M5	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Navl	AGCACGAGCCTA	CATGCTGCCTCCCGTAGGAGT	F11Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Navl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Umbilicus	sample267	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Fcsw	ACACACTATGGC	CATGCTGCCTCCCGTAGGAGT	M11Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Fcsw	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample495	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M1	M1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M12Nstl	ACTAGCTCCATA	CATGCTGCCTCCCGTAGGAGT	M12Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Nstl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample156	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M44Frhd	TAACAGTCGCTG	CATGCTGCCTCCCGTAGGAGT	M44Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M44Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Forehead	sample060	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Fcsp	AATCGTGACTCG	CATGCTGCCTCCCGTAGGAGT	M11Fcsp	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Fcsp	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample494	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M1	M1	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F21Indl	ATCTCTGGCATA	CATGCTGCCTCCCGTAGGAGT	F21Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Indl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left index finger	sample137	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M13Nost	CTTGTGTCGATA	CATGCTGCCTCCCGTAGGAGT	M13Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M13Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Nares	sample285	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M1	M1	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M22Mout	CGAGGCTCAGTA	CATGCTGCCTCCCGTAGGAGT	M22Mout	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Mout	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Oral cavity	sample262	False	UBERON:oral cavity	UBERON:saliva	UBERON:mouth	2008-2009	human oral metagenome	mouth	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M2	M2	9606	40.0149856	-105.2705456	oral cavity	False	True	water_rinse	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.F21Nose	ATGACTCATTCG	CATGCTGCCTCCCGTAGGAGT	F21Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Nose	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:External nose	sample021	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M24Fcsw	GCATAGTAGCCG	CATGCTGCCTCCCGTAGGAGT	M24Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample505	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M2	M2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.M41Plmr	GACAGTTACTGC	CATGCTGCCTCCCGTAGGAGT	M41Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Plmr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right palm	sample436	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Urin	GACGCAGTAGCT	CATGCTGCCTCCCGTAGGAGT	M41Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Urin	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample565	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M4	M4	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M41Plml	GACAGGAGATAG	CATGCTGCCTCCCGTAGGAGT	M41Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Plml	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left palm	sample213	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Indr	ATCTGAGCTGGT	CATGCTGCCTCCCGTAGGAGT	F21Indr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Indr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right index finger	sample359	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	right index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F11Indl	AGATCGGCTCGA	CATGCTGCCTCCCGTAGGAGT	F11Indl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Indl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left index finger	sample135	False	UBERON:skin	UBERON:sebum	UBERON:skin of finger	2008-2009	human skin metagenome	left index finger	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F1	F1	9606	40.0149856	-105.2705456	left palmar index finger	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Forr	CTATCTAGCGAG	CATGCTGCCTCCCGTAGGAGT	M32Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Forr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Surface of right arm	sample354	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Fotl	ATGGATACGCTC	CATGCTGCCTCCCGTAGGAGT	F21Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Fotl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left foot surface	sample225	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Aptr	AACTCGTCGATG	CATGCTGCCTCCCGTAGGAGT	M11Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Aptr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right axilla	sample321	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F31Urin	GCATTGCGTGAG	CATGCTGCCTCCCGTAGGAGT	F31Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F31Urin	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample561	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F3	F3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M63Fotr	TATGCACCAGTG	CATGCTGCCTCCCGTAGGAGT	M63Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M63Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Right foot surface	sample474	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F21Fotr	ATGGCAGCTCTA	CATGCTGCCTCCCGTAGGAGT	F21Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F21Fotr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right foot surface	sample448	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M14Urin	GACGTTGCACAG	CATGCTGCCTCCCGTAGGAGT	M14Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample582	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M1	M1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M14Uric	GACTAACGTCAC	CATGCTGCCTCCCGTAGGAGT	M14Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M14Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample581	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M1	M1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M42Nstr	GAGTAGCTCGTG	CATGCTGCCTCCCGTAGGAGT	M42Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Nstr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample384	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M32Ewxr	CTAGGTCACTAG	CATGCTGCCTCCCGTAGGAGT	M32Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Ewxr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right external auditory canal	sample409	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M24Plmr	GCAATAGCTGCT	CATGCTGCCTCCCGTAGGAGT	M24Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right palm	sample431	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Aptr	CGCGTAACTGTA	CATGCTGCCTCCCGTAGGAGT	M31Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Aptr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right axilla	sample325	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Aptl	ATGTACGGCGAC	CATGCTGCCTCCCGTAGGAGT	F22Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Aptl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left axilla	sample096	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M43Fotr	GTGTACCTATCA	CATGCTGCCTCCCGTAGGAGT	M43Fotr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Fotr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right foot surface	sample470	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	right sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	right plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M41Nose	GAATGATGAGTG	CATGCTGCCTCCCGTAGGAGT	M41Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M41Nose	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:External nose	sample031	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Aptl	ACCTGTCTCTCT	CATGCTGCCTCCCGTAGGAGT	M12Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Aptl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left axilla	sample100	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M1	M1	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M12Aptr	ACGACGTCTTAG	CATGCTGCCTCCCGTAGGAGT	M12Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M12Aptr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Right axilla	sample322	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M1	M1	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F24Frhd	GCTAAGAGAGTA	CATGCTGCCTCCCGTAGGAGT	F24Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F24Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Forehead	sample040	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F2	F2	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M43Fotl	GTGTCTACATTG	CATGCTGCCTCCCGTAGGAGT	M43Fotl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M43Fotl	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left foot surface	sample247	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of foot	2008-2009	human skin metagenome	left sole of foot	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left plantar foot	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M31Aptl	CGCGATAGCAGT	CATGCTGCCTCCCGTAGGAGT	M31Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M31Aptl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left axilla	sample103	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Aptr	ATGTCACCGTGA	CATGCTGCCTCCCGTAGGAGT	F22Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Aptr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right axilla	sample318	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M24Plml	GCACATCGAGCA	CATGCTGCCTCCCGTAGGAGT	M24Plml	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Plml	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left palm	sample208	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	left palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left palm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M42Nstl	GAGGCTCATCAT	CATGCTGCCTCCCGTAGGAGT	M42Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M42Nstl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Nares	sample162	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M4	M4	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F32Labi	GCTATTCGACAT	CATGCTGCCTCCCGTAGGAGT	F32Labi	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Labi	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Frenulum of labia minora	sample092	False	UBERON:skin	UBERON:mucus	UBERON:labia minora	2008-2009	human skin metagenome	labia minora	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:mucus	Negative	human	F3	F3	9606	40.0149856	-105.2705456	labia minora	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M53Uric	TAGAGAGAGTGG	CATGCTGCCTCCCGTAGGAGT	M53Uric	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Uric	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Urine	sample595	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M5	M5	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F32Kner	GCGACTTGTGTA	CATGCTGCCTCCCGTAGGAGT	F32Kner	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Kner	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right popliteal fossa	sample334	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	right back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M32Aptr	CTACTGATATCG	CATGCTGCCTCCCGTAGGAGT	M32Aptr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Aptr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right axilla	sample326	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	right armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M22Navl	CGAGTCTAGTTG	CATGCTGCCTCCCGTAGGAGT	M22Navl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Navl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Umbilicus	sample275	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of abdomen	2008-2009	human skin metagenome	navel	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	umbilicus	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M53Urin	TAGACTGTACTC	CATGCTGCCTCCCGTAGGAGT	M53Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M53Urin	0.006	V2	0	FKB0RMH	CGS-GL	8/20/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	60.0	years	0	FMA:Urine	sample596	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M5	M5	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.F22Urin	CAGAGGAGCTCT	CATGCTGCCTCCCGTAGGAGT	F22Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Urin	0.006	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Urine	sample556	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F2	F2	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M22Ewxl	CCGACTGAGATG	CATGCTGCCTCCCGTAGGAGT	M22Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Ewxl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left external auditory canal	sample184	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M32Aptl	CTACTACAGGTG	CATGCTGCCTCCCGTAGGAGT	M32Aptl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Aptl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left axilla	sample104	False	UBERON:skin	UBERON:sebum	UBERON:skin of arm	2008-2009	human skin metagenome	left armpit	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sweat	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left axilla	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M23Fcsw	GATTAGCACTCT	CATGCTGCCTCCCGTAGGAGT	M23Fcsw	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Fcsw	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Feces	sample504	False	UBERON:feces	UBERON:feces	UBERON:feces	2008-2009	human gut metagenome	stool	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:feces	Negative	human	M2	M2	9606	40.0149856	-105.2705456	stool	False	True		XXQIITAXX	male	408170	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human gut metagenome
449.F32Knel	GCCTATACTACA	CATGCTGCCTCCCGTAGGAGT	F32Knel	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Knel	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Left popliteal fossa	sample112	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of knee	2008-2009	human skin metagenome	left back of knees	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	left popliteal fossa	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Ewxl	ATTATCGTGCAC	CATGCTGCCTCCCGTAGGAGT	F22Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Ewxl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Left external auditory canal	sample179	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F2	F2	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M24Frhd	GCACGACAACAC	CATGCTGCCTCCCGTAGGAGT	M24Frhd	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M24Frhd	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Forehead	sample052	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of head	2008-2009	human skin metagenome	forehead	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	forehead	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M23Ewax	GATGATCGCCGA	CATGCTGCCTCCCGTAGGAGT	M23Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M23Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:External auditory canal	sample305	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M2	M2	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M22Glns	CGACATGCTATT	CATGCTGCCTCCCGTAGGAGT	M22Glns	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M22Glns	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Glans penis	sample068	False	UBERON:skin	UBERON:sebum	UBERON:glans penis	2008-2009	human skin metagenome	glans penis	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	glans penis	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M34Tong	GTAGATGCTTCG	CATGCTGCCTCCCGTAGGAGT	M34Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M34Tong	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample544	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	M3	M3	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	male	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M21Nose	CATATCGCAGTT	CATGCTGCCTCCCGTAGGAGT	M21Nose	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Nose	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:External nose	sample027	False	UBERON:skin	UBERON:sebum	UBERON:nose	2008-2009	human skin metagenome	external nose	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	external nose	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.F22Ewxr	ATTCTGTGAGCG	CATGCTGCCTCCCGTAGGAGT	F22Ewxr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F22Ewxr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	31.0	years	0	FMA:Right external auditory canal	sample402	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	right outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	F2	F2	9606	40.0149856	-105.2705456	right external auditory canal	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F32Urin	GGCAGTGTATCG	CATGCTGCCTCCCGTAGGAGT	F32Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F32Urin	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Urine	sample562	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	F3	F3	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	female	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M32Nstl	CTCGCACATATA	CATGCTGCCTCCCGTAGGAGT	M32Nstl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Nstl	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample160	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	left nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	left naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M64Ewax	TCAGCTCAACTA	CATGCTGCCTCCCGTAGGAGT	M64Ewax	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Ewax	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:External auditory canal	sample314	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:zone of skin of outer ear	2008-2009	human metagenome	outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M6	M6	9606	40.0149856	-105.2705456	external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.M32Nstr	CTCGTGGAGTAG	CATGCTGCCTCCCGTAGGAGT	M32Nstr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M32Nstr	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Nares	sample382	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	right nostril	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M3	M3	9606	40.0149856	-105.2705456	right naris	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.F34Plmr	GTCGCTGTCTTC	CATGCTGCCTCCCGTAGGAGT	F34Plmr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F34Plmr	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Right palm	sample423	False	UBERON:skin	UBERON:sebum	UBERON:zone of skin of hand	2008-2009	human skin metagenome	right palm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	F3	F3	9606	40.0149856	-105.2705456	right palm	False	True		XXQIITAXX	female	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
449.M11Urin	ACCTCGATCAGA	CATGCTGCCTCCCGTAGGAGT	M11Urin	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial variation in human body habitats across space and time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M11Urin	0.006	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Urine	sample557	False	UBERON:urine	UBERON:urine	UBERON:urine	2008-2009	human urine metagenome	urine	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:urine	Negative	human	M1	M1	9606	40.0149856	-105.2705456	urine	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human urine metagenome
449.M21Ewxl	CAGCGGTGACAT	CATGCTGCCTCCCGTAGGAGT	M21Ewxl	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Ewxl	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Left external auditory canal	sample183	False	UBERON:external auditory canal	UBERON:cerumen	UBERON:ear canal	2008-2009	human metagenome	left outer ear canal/earwax	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:ear wax	Negative	human	M2	M2	9606	40.0149856	-105.2705456	left external auditory canal	False	True		XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human metagenome
449.F11Tong	AGCTCCATACAG	CATGCTGCCTCCCGTAGGAGT	F11Tong	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	F11Tong	0.005	V2	0	FFLHOYS	CGS-GL	8/18/2008	FFLHOYS	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	33.0	years	0	FMA:Dorsal surface of tongue	sample521	False	UBERON:oral cavity	UBERON:saliva	UBERON:tongue	2008-2009	human oral metagenome	tongue	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:saliva	Negative	human	F1	F1	9606	40.0149856	-105.2705456	dorsal surface of tongue	False	True	swab	XXQIITAXX	female	447426	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human oral metagenome
449.M64Nost	TCACTTCTCGCT	CATGCTGCCTCCCGTAGGAGT	M64Nost	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M64Nost	0.006	V2	0	FKB0RMH	CGS-GL	11/14/2008	FKB0RMH	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486		years	0	FMA:Nares	sample296	False	UBERON:nostril	UBERON:mucus	UBERON:nostril	2008-2009	human nose metagenome	nostrils	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M6	M6	9606	40.0149856	-105.2705456	nares	False	True	swab	XXQIITAXX	male	646099	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human nose metagenome
449.M21Forr	CAGTCGAAGCTG	CATGCTGCCTCCCGTAGGAGT	M21Forr	True	CostelloWholeBodySites	CCME	Healthy adults were recruited to donate samples on two consecutive days in June and again three months later on two consecutive days in September 2008. Volunteers were unrelated individuals of both sexes and most lived in Boulder, CO. Female subjects F1, F2, F3 and male subjects M1, M2, M3, M4, and M6 were 30-35 years old. Subject M5 was approximately 60 years old. The health status of the volunteers was self-reported. None of the volunteers indicated that they had been hospitalized in the previous 6 months. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0708.12). On the day of sampling, participants were instructed to bathe in the morning using their choice of personal hygiene products, but to avoid wearing deodorant or antiperspirant. The interval between subject bathing and the collection of most samples likely ranged from around several hours to half an hour. Participants were asked to avoid eating or drinking for one hour prior to oral sampling. Skin surfaces, hair on top of the head, and nostrils (nares) were sampled using autoclaved cotton-tipped swabs (Puritan) pre-moistened with a sterile solution of 0.15 M NaCl and 0.1% Tween 20 (S1, S2). Swabbing has been shown to be a suitable method for skin sample collection for microbial community analysis (S3). Dry cotton-tipped swabs were used to sample the external auditory canal [and earwax (cerumen) if present], the dorsal surface of the tongue, and stool. Stool samples have been shown to provide an adequately representative sample of the gut microbiota (S4). Stool was swabbed using two different methods for comparison: i) off of used bathroom tissue and ii) by stabbing the swab directly into the largest piece of feces (see Fig. S22 for comparison). We found that swabbing off of used bathroom tissue was adequate for obtaining material for microbial community analysis. Swabs were placed in sterile 15 ml plastic tubes and stored at -80C within 10 minutes of sampling. Volunteers sampled stool on the same days that the other samples were collected (within 24 hours). If needed, the subjects were provided dry ice for the transport of their stool samples back to the lab. Liquid samples were also collected. The oral cavity was rinsed by swishing 10 ml of sterile water for 10 seconds, and then spitting the water into a sterile 50 ml plastic tube (see Fig. S22 for comparison to dorsal tongue swabs). Liquids were stored at 4C for several hours before sterile filtration onto 0.2micro-m pore size cellulose-nitrate filters (Nalgene). Filtered samples were immediately placed at -80C. Volunteers sampled themselves while wearing sterile gloves after first having their palms and index fingers swabbed by another person wearing sterile gloves. Replicate samples from the right and left sides of the body were taken when possible. All but one subject had not taken antibiotics in the 6 months prior to the June sampling dates, and none took antibiotics during the study period. Figure S1 lists the sample types, dates, and subjects. Samples were stored at -80C for <1 week prior to DNA extraction. We performed a follow-up study aimed at addressing whether skin location influences bacterial community assembly. Our approach involved transplanting foreign bacteria from various donor sites (dorsal tongue, forehead, and volar forearm) onto disinfected recipient skin sites (forehead and volar forearm) both within and between individuals. All individuals were made aware of the nature of the experiment and gave written informed consent in accordance with the sampling protocol approved by the University of Colorado Human Research Committee (protocol 0109.23).	Bacterial Community Variation in Human Body Habitats Across Space and Time	TCAG	Amplicon DNA concentrations were determined using the Quant-iT PicoGreen dsDNA reagent and kit (Invitrogen). Assays were carried out using 5-10 _l of cleaned PCR product in a total reaction volume of 200 _l in black, 96-well microtiter plates. Fluorescence was measured on a BioTek Synergy HT plate reader using the 480/520-nm excitation/emission filter pair. Following quantitation, cleaned amplicons were combined in equimolar ratios into a single tube. The final pool of DNA was precipitated on ice for 45 minutes following theaddition of 5 M NaCl (0.2 M final concentration) and 2 volumes of ice-cold 100% ethanol. The precipitated DNA was centrifuged at 7,800 x g for 40 minutes at 4C, and the resulting pellet was washed with an equal volume of ice-cold 70% ethanol and centrifuged again at 7,800 x g for 20 minutes at 4C. The supernatant was removed and the pellet was air dried for 10 minutes at room temperature and then resuspended in 100 micro-l of nuclease-free water (MO BIO). The final concentration of the pooled DNA was determined using a NanoDrop spectrophotometer (Thermo Fisher). Pyrosequencing was carried out using primer A on a 454 Life Sciences Genome Sequencer FLX instrument (Roche).	CA	PMID: 19892944	http://www.mobio.com/soil-dna-isolation/powersoil-dna-isolation-kit.html	initial denaturation: 94; annealing: 50_0.5; elongation: 72_1.5; final elongation: 72_10; 35	FWD:GCCTTGCCAGCCCGCTCAGTCAGAGTTTGATCCTGGCTCAG;REV:CATGCTGCCTCCCGTAGGAGT	False	FLX	M21Forr	0.006	V2	0	FFO92CG	CGS-GL	8/20/2008	FFO92CG	swab with sterile saline	1, swab	CCME	XXQIITAXX	pyrosequencing	CCME	costello_whole_body_sites	16S rRNA	V2	http://www.scienceonline.org/cgi/content/abstract/1177486	36.0	years	0	FMA:Surface of right arm	sample351	False	UBERON:skin	UBERON:sebum	UBERON:skin of forearm	2008-2009	human skin metagenome	right forearm	GAZ:United States of America	0	True	1624.097656	ENVO:urban biome	ENVO:human-associated habitat	ENVO:sebum	Negative	human	M2	M2	9606	40.0149856	-105.2705456	right volar forearm	False	True		XXQIITAXX	male	539655	Bacterial Community Variation in Human Body Habitats Across Space and Time	Bacterial community variation in human body habitats across space and time	CostelloWholeBodySites	Gail Ackermann	Rob Knight	human skin metagenome
