Sewage Reflects the Microbiomes of Human Populations

ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations sca...

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Autores principales:	Ryan J. Newton, Sandra L. McLellan, Deborah K. Dila, Joseph H. Vineis, Hilary G. Morrison, A. Murat Eren, Mitchell L. Sogin
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2015
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/5b2def97e3744ddd90a564d2bff938e3
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spelling	oai:doaj.org-article:5b2def97e3744ddd90a564d2bff938e32021-11-15T15:41:33ZSewage Reflects the Microbiomes of Human Populations10.1128/mBio.02574-142150-7511https://doaj.org/article/5b2def97e3744ddd90a564d2bff938e32015-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02574-14https://doaj.org/toc/2150-7511ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. IMPORTANCE The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However, financial considerations and privacy concerns limit the number of individuals who can be screened. By analyzing sewage from 71 cities, we demonstrate that geographically distributed U.S. populations share a small set of bacteria whose members represent various common community states within U.S. adults. Cities were differentiated by their sewage bacterial communities, and the community structures were good predictors of a city's estimated level of obesity. Our approach demonstrates the use of sewage as a means to sample the fecal microbiota from millions of people and its potential to elucidate microbiome patterns associated with human demographics.Ryan J. NewtonSandra L. McLellanDeborah K. DilaJoseph H. VineisHilary G. MorrisonA. Murat ErenMitchell L. SoginAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 6, Iss 2 (2015)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Ryan J. Newton Sandra L. McLellan Deborah K. Dila Joseph H. Vineis Hilary G. Morrison A. Murat Eren Mitchell L. Sogin Sewage Reflects the Microbiomes of Human Populations
description	ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. IMPORTANCE The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However, financial considerations and privacy concerns limit the number of individuals who can be screened. By analyzing sewage from 71 cities, we demonstrate that geographically distributed U.S. populations share a small set of bacteria whose members represent various common community states within U.S. adults. Cities were differentiated by their sewage bacterial communities, and the community structures were good predictors of a city's estimated level of obesity. Our approach demonstrates the use of sewage as a means to sample the fecal microbiota from millions of people and its potential to elucidate microbiome patterns associated with human demographics.
format	article
author	Ryan J. Newton Sandra L. McLellan Deborah K. Dila Joseph H. Vineis Hilary G. Morrison A. Murat Eren Mitchell L. Sogin
author_facet	Ryan J. Newton Sandra L. McLellan Deborah K. Dila Joseph H. Vineis Hilary G. Morrison A. Murat Eren Mitchell L. Sogin
author_sort	Ryan J. Newton
title	Sewage Reflects the Microbiomes of Human Populations
title_short	Sewage Reflects the Microbiomes of Human Populations
title_full	Sewage Reflects the Microbiomes of Human Populations
title_fullStr	Sewage Reflects the Microbiomes of Human Populations
title_full_unstemmed	Sewage Reflects the Microbiomes of Human Populations
title_sort	sewage reflects the microbiomes of human populations
publisher	American Society for Microbiology
publishDate	2015
url	https://doaj.org/article/5b2def97e3744ddd90a564d2bff938e3
work_keys_str_mv	AT ryanjnewton sewagereflectsthemicrobiomesofhumanpopulations AT sandralmclellan sewagereflectsthemicrobiomesofhumanpopulations AT deborahkdila sewagereflectsthemicrobiomesofhumanpopulations AT josephhvineis sewagereflectsthemicrobiomesofhumanpopulations AT hilarygmorrison sewagereflectsthemicrobiomesofhumanpopulations AT amurateren sewagereflectsthemicrobiomesofhumanpopulations AT mitchelllsogin sewagereflectsthemicrobiomesofhumanpopulations
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Sewage Reflects the Microbiomes of Human Populations

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