Structure, function and diversity of the healthy human microbiome.

TitleStructure, function and diversity of the healthy human microbiome.
Publication TypeJournal Article
Year of Publication2012
Corporate AuthorsConsortium, HMicrobiome
JournalNature
Volume486
Issue7402
Pagination207-14
Date Published2012 Jun 14
ISSN1476-4687
KeywordsAdolescent, Adult, Bacteria, Biodiversity, Ecosystem, Female, Health, Humans, Male, Metabolic Networks and Pathways, Metagenome, Metagenomics, Phenotype, RNA, Ribosomal, 16S, Young Adult
Abstract

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

DOI10.1038/nature11234
Alternate JournalNature
PubMed ID22699609
PubMed Central IDPMC3564958
Grant ListDP2 OD001500 / OD / NIH HHS / United States
DP2OD001500 / OD / NIH HHS / United States
N01AI30071 / AI / NIAID NIH HHS / United States
N01AI30071 / AI / NIAID NIH HHS / United States
N01HG62088 / HG / NHGRI NIH HHS / United States
N01HG62088 / HG / NHGRI NIH HHS / United States
P30 DE020751 / DE / NIDCR NIH HHS / United States
P30DE020751 / DE / NIDCR NIH HHS / United States
R01 DE021574 / DE / NIDCR NIH HHS / United States
R01 HG004853 / HG / NHGRI NIH HHS / United States
R01 HG004856 / HG / NHGRI NIH HHS / United States
R01 HG004857 / HG / NHGRI NIH HHS / United States
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R01 HG004885 / HG / NHGRI NIH HHS / United States
R01 HG004900 / HG / NHGRI NIH HHS / United States
R01 HG004906 / HG / NHGRI NIH HHS / United States
R01 HG004908 / HG / NHGRI NIH HHS / United States
R01 HG005171 / HG / NHGRI NIH HHS / United States
R01 HG005172 / HG / NHGRI NIH HHS / United States
R01 HG005969 / HG / NHGRI NIH HHS / United States
R01 HG005975 / HG / NHGRI NIH HHS / United States
R01DE021574 / DE / NIDCR NIH HHS / United States
R01HG004853 / HG / NHGRI NIH HHS / United States
R01HG004856 / HG / NHGRI NIH HHS / United States
R01HG004857 / HG / NHGRI NIH HHS / United States
R01HG004872 / HG / NHGRI NIH HHS / United States
R01HG004877 / HG / NHGRI NIH HHS / United States
R01HG004885 / HG / NHGRI NIH HHS / United States
R01HG004900 / HG / NHGRI NIH HHS / United States
R01HG004906 / HG / NHGRI NIH HHS / United States
R01HG004908 / HG / NHGRI NIH HHS / United States
R01HG005171 / HG / NHGRI NIH HHS / United States
R01HG005172 / HG / NHGRI NIH HHS / United States
R01HG005969 / HG / NHGRI NIH HHS / United States
R01HG005975 / HG / NHGRI NIH HHS / United States
R21 CA139193 / CA / NCI NIH HHS / United States
R21CA139193 / CA / NCI NIH HHS / United States
R21HG005811 / HG / NHGRI NIH HHS / United States
R37 DE016937 / DE / NIDCR NIH HHS / United States
RC1 DE020298 / DE / NIDCR NIH HHS / United States
RC1DE0202098 / DE / NIDCR NIH HHS / United States
T32AI007528 / AI / NIAID NIH HHS / United States
U01 DE016937 / DE / NIDCR NIH HHS / United States
U01 HG004866 / HG / NHGRI NIH HHS / United States
U01DE016937 / DE / NIDCR NIH HHS / United States
U01HG004866 / HG / NHGRI NIH HHS / United States
U54 AI084844 / AI / NIAID NIH HHS / United States
U54 HG003067 / HG / NHGRI NIH HHS / United States
U54 HG003079 / HG / NHGRI NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
U54 HG004968 / HG / NHGRI NIH HHS / United States
U54 HG004969 / HG / NHGRI NIH HHS / United States
U54 HG004973 / HG / NHGRI NIH HHS / United States
U54AI084844 / AI / NIAID NIH HHS / United States
U54HG003067 / HG / NHGRI NIH HHS / United States
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U54HG004973 / HG / NHGRI NIH HHS / United States
UH2 AI083263 / AI / NIAID NIH HHS / United States
UH2 AR057504 / AR / NIAMS NIH HHS / United States
UH2 DK083990 / DK / NIDDK NIH HHS / United States
UH2AI083263 / AI / NIAID NIH HHS / United States
UH2AR057504 / AR / NIAMS NIH HHS / United States
UH2AR057506 / AR / NIAMS NIH HHS / United States
UH2DK083990 / DK / NIDDK NIH HHS / United States
UH3 AI083263 / AI / NIAID NIH HHS / United States
UH3 DK083993 / DK / NIDDK NIH HHS / United States
UH3AI083263 / AI / NIAID NIH HHS / United States
UH3AR057504 / AR / NIAMS NIH HHS / United States
UH3DK083993 / DK / NIDDK NIH HHS / United States
/ / Howard Hughes Medical Institute / United States