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PMID: 22699610 Published · epublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

A framework for human microbiome research.

Nature ·Vol. 486 ·No. 7402 ·2012-06-13 ·Pages 215-21

Human Microbiome Project Consortium

Abstract

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

MeSH Terms
Adolescent Adult Bacteria/genetics Female Humans Male Metagenome Metagenomics/methods RNA, Ribosomal, 16S/genetics Reference Standards Statistics as Topic Young Adult
Chemicals
RNA, Ribosomal, 16S
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Human Microbiome Project Consortium
Investigators
248 investigators, click to expand
Methé Barbara A
Nelson Karen E
Pop Mihai
Creasy Heather H
Giglio Michelle G
Huttenhower Curtis
Gevers Dirk
Petrosino Joseph F
Abubucker Sahar
Badger Jonathan H
Chinwalla Asif T
Earl Ashlee M
FitzGerald Michael G
Fulton Robert S
Hallsworth-Pepin Kymberlie
Lobos Elizabeth A
Madupu Ramana
Magrini Vincent
Martin John C
Mitreva Makedonka
Muzny Donna M
Sodergren Erica J
Versalovic James
Wollam Aye M
Worley Kim C
Wortman Jennifer R
Young Sarah K
Zeng Qiandong
Aagaard Kjersti M
Abolude Olukemi O
Allen-Vercoe Emma
Alm Eric J
Alvarado Lucia
Andersen Gary L
Anderson Scott
Appelbaum Elizabeth
Arachchi Harindra M
Armitage Gary
Arze Cesar A
Ayvaz Tulin
Baker Carl C
Begg Lisa
Belachew Tsegahiwot
Bhonagiri Veena
Bihan Monika
Blaser Martin J
Bloom Toby
Bonazzi Vivien R
Brooks Paul
Buck Gregory A
Buhay Christian J
Busam Dana A
Campbell Joseph L
Canon Shane R
Cantarel Brandi L
Chain Patrick S
Chen I-Min A
Chen Lei
Chhibba Shaila
Chu Ken
Ciulla Dawn M
Clemente Jose C
Clifton Sandra W
Conlan Sean
Crabtree Jonathan
Cutting Mary A
Davidovics Noam J
Davis Catherine C
DeSantis Todd Z
Deal Carolyn
Delehaunty Kimberley D
Dewhirst Floyd E
Deych Elena
Ding Yan
Dooling David J
Dugan Shannon P
Dunne W Michael
Durkin A Scott
Edgar Robert C
Erlich Rachel L
Farmer Candace N
Farrell Ruth M
Faust Karoline
Feldgarden Michael
Felix Victor M
Fisher Sheila
Fodor Anthony A
Forney Larry
Foster Leslie
Di Francesco Valentina
Friedman Jonathan
Friedrich Dennis C
Fronick Catrina C
Fulton Lucinda L
Gao Hongyu
Garcia Nathalia
Giannoukos Georgia
Giblin Christina
Giovanni Maria Y
Goldberg Jonathan M
Goll Johannes
Gonzalez Antonio
Griggs Allison
Gujja Sharvari
Haas Brian J
Hamilton Holli A
Harris Emily L
Hepburn Theresa A
Herter Brandi
Hoffmann Diane E
Holder Michael E
Howarth Clinton
Huang Katherine H
Huse Susan M
Izard Jacques
Jansson Janet K
Jiang Huaiyang
Jordan Catherine
Joshi Vandita
Katancik James A
Keitel Wendy A
Kelley Scott T
Kells Cristyn
Kinder-Haake Susan
King Nicholas B
Knight Rob
Knights Dan
Kong Heidi H
Koren Omry
Koren Sergey
Kota Karthik C
Kovar Christie L
Kyrpides Nikos C
La Rosa Patricio S
Lee Sandra L
Lemon Katherine P
Lennon Niall
Lewis Cecil M
Lewis Lora
Ley Ruth E
Li Kelvin
Liolios Konstantinos
Liu Bo
Liu Yue
Lo Chien-Chi
Lozupone Catherine A
Lunsford R Dwayne
Madden Tessa
Mahurkar Anup A
Mannon Peter J
Mardis Elaine R
Markowitz Victor M
Mavrommatis Konstantinos
McCorrison Jamison M
McDonald Daniel
McEwen Jean
McGuire Amy L
McInnes Pamela
Mehta Teena
Mihindukulasuriya Kathie A
Miller Jason R
Minx Patrick J
Newsham Irene
Nusbaum Chad
O'Laughlin Michelle
Orvis Joshua
Pagani Ioanna
Palaniappan Krishna
Patel Shital M
Pearson Matthew
Peterson Jane
Podar Mircea
Pohl Craig
Pollard Katherine S
Priest Margaret E
Proctor Lita M
Qin Xiang
Raes Jeroen
Ravel Jacques
Reid Jeffrey G
Rho Mina
Rhodes Rosamond
Riehle Kevin P
Rivera Maria C
Rodriguez-Mueller Beltran
Rogers Yu-Hui
Ross Matthew C
Russ Carsten
Sanka Ravi K
Sankar Pamela
Sathirapongsasuti J Fah
Schloss Jeffery A
Schloss Patrick D
Schmidt Thomas M
Scholz Matthew
Schriml Lynn
Schubert Alyxandria M
Segata Nicola
Segre Julia A
Shannon William D
Sharp Richard R
Sharpton Thomas J
Shenoy Narmada
Sheth Nihar U
Simone Gina A
Singh Indresh
Smillie Chris S
Sobel Jack D
Sommer Daniel D
Spicer Paul
Sutton Granger G
Sykes Sean M
Tabbaa Diana G
Thiagarajan Mathangi
Tomlinson Chad M
Torralba Manolito
Treangen Todd J
Truty Rebecca M
Vishnivetskaya Tatiana A
Walker Jason
Wang Lu
Wang Zhengyuan
Ward Doyle V
Warren Wesley
Watson Mark A
Wellington Christopher
Wetterstrand Kris A
White James R
Wilczek-Boney Katarzyna
Wu Yuan Qing
Wylie Kristine M
Wylie Todd
Yandava Chandri
Ye Liang
Ye Yuzhen
Yooseph Shibu
Youmans Bonnie P
Zhang Lan
Zhou Yanjiao
Zhu Yiming
Zoloth Laurie
Zucker Jeremy D
Birren Bruce W
Gibbs Richard A
Highlander Sarah K
Weinstock George M
Wilson Richard K
White Owen
References (18)
18 references, click to expand
  1. Metabolic reconstruction for metagenomic data and its application to the human microbiome.
    PLoS Comput Biol. 2012;8(6):e1002358 PMID: 22719234
  2. Microbial metagenomics: beyond the genome.
    Ann Rev Mar Sci. 2011;3:347-71 PMID: 21329209
  3. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.
    Environ Microbiol. 2010 Jan;12(1):118-23 PMID: 19725865
  4. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.
    Appl Environ Microbiol. 2009 Dec;75(23):7537-41 PMID: 19801464
  5. Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem.
    J Math Biol. 2013 Nov;67(5):1141-61 PMID: 22965653
  6. A human gut microbial gene catalogue established by metagenomic sequencing.
    Nature. 2010 Mar 4;464(7285):59-65 PMID: 20203603
  7. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
    Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
  8. Evaluation of 16S rDNA-based community profiling for human microbiome research.
    PLoS One. 2012;7(6):e39315 PMID: 22720093
  9. Search and clustering orders of magnitude faster than BLAST.
    Bioinformatics. 2010 Oct 1;26(19):2460-1 PMID: 20709691
  10. Hypothesis testing and power calculations for taxonomic-based human microbiome data.
    PLoS One. 2012;7(12):e52078 PMID: 23284876
  11. A catalog of reference genomes from the human microbiome.
    Science. 2010 May 21;328(5981):994-9 PMID: 20489017
  12. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.
    PLoS One. 2011;6(12):e27310 PMID: 22194782
  13. Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities.
    PLoS One. 2012;7(6):e36427 PMID: 22719831
  14. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D190-5 PMID: 19900971
  15. Accuracy and quality of massively parallel DNA pyrosequencing.
    Genome Biol. 2007;8(7):R143 PMID: 17659080
  16. A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).
    PLoS One. 2012;7(6):e29044 PMID: 22719821
  17. QIIME allows analysis of high-throughput community sequencing data.
    Nat Methods. 2010 May;7(5):335-6 PMID: 20383131
  18. The NIH Human Microbiome Project.
    Genome Res. 2009 Dec;19(12):2317-23 PMID: 19819907
Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
DOI
10.1038/nature11209
Published
2012-06-13
Epub
2012-00-13
Pages
215-21
Language
English
Region
England
NLM ID
0410462
PMCID
PMC3377744
Subset
IM
Grants
NHGRI NIH HHS · R01HG004856 · United States
NHGRI NIH HHS · R01HG004908 · United States
NIDCR NIH HHS · P30DE020751 · United States
NHGRI NIH HHS · R21HG005811 · United States
NHGRI NIH HHS · R01HG005172 · United States
NIDDK NIH HHS · UH3DK083993 · United States
NHGRI NIH HHS · R01 HG005969 · United States
NHGRI NIH HHS · R01HG004900 · United States
NIDDK NIH HHS · UH2 DK083990 · United States
NHGRI NIH HHS · N01HG62088 · United States
NHGRI NIH HHS · R01 HG004857 · United States
NHGRI NIH HHS · U54 HG004973 · United States
NIDCR NIH HHS · U01DE016937 · United States
NIDCR NIH HHS · RC1DE020298 · United States
NIAMS NIH HHS · UH2 AR057504 · United States
NHGRI NIH HHS · U54HG004969 · United States
NIAID NIH HHS · T32 AI007528 · United States
NHGRI NIH HHS · U54 HG003067 · United States
NHGRI NIH HHS · U54HG003273 · United States
NHGRI NIH HHS · R01HG004877 · United States
NHGRI NIH HHS · R01 HG004900 · United States
NIH HHS · DP2OD001500 · United States
NHGRI NIH HHS · R01HG004885 · United States
NHGRI NIH HHS · R01HG004872 · United States
NHGRI NIH HHS · R01 HG004856 · United States
NHGRI NIH HHS · R01 HG005171 · United States
NIAID NIH HHS · UH3AI083263 · United States
NIAMS NIH HHS · UH2 AR057506 · United States
Howard Hughes Medical Institute · United States
NIAMS NIH HHS · UH2AR057504 · United States
NHGRI NIH HHS · U01HG004866 · United States
NHGRI NIH HHS · U54HG003067 · United States
NIAID NIH HHS · U54 AI084844 · United States
NIAMS NIH HHS · UH3AR057504 · United States
NHGRI NIH HHS · U54 HG003273 · United States
NIAID NIH HHS · UH2AI083263 · United States
NHGRI NIH HHS · U01 HG004866 · United States
NIAID NIH HHS · U54AI084844 · United States
NHGRI NIH HHS · R01 HG005975 · United States
NIDCR NIH HHS · R37 DE016937 · United States
NIDDK NIH HHS · UH3 DK083993 · United States
NIDCR NIH HHS · R01DE021574 · United States
NHGRI NIH HHS · R01 HG004885 · United States
NHGRI NIH HHS · U54 HG004968 · United States
NHGRI NIH HHS · U54HG004973 · United States
NIAID NIH HHS · UH2 AI083263 · United States
NHGRI NIH HHS · R01HG005171 · United States
NIAID NIH HHS · T32AI007528 · United States
NHGRI NIH HHS · R01HG004906 · United States
NHGRI NIH HHS · U54HG003079 · United States
NIDCR NIH HHS · RC1 DE020298 · United States
NIH HHS · DP2 OD001500 · United States
NIDCR NIH HHS · R01 DE021574 · United States
NIGMS NIH HHS · T32 GM087237 · United States
NHGRI NIH HHS · R01 HG004908 · United States
NHGRI NIH HHS · R01 HG004872 · United States
NCI NIH HHS · R21 CA139193 · United States
NHGRI NIH HHS · R01HG005975 · United States
NIDCR NIH HHS · U01 DE016937 · United States
NCI NIH HHS · R21CA139193 · United States
NHGRI NIH HHS · R21 HG005811 · United States
NHGRI NIH HHS · U54 HG003079 · United States
NHGRI NIH HHS · R01 HG004853 · United States
NIAID NIH HHS · N01AI30071 · United States
NHGRI NIH HHS · U54 HG004969 · United States
NHGRI NIH HHS · R01HG00485 · United States
NHGRI NIH HHS · R01HG004853 · United States
NIAID NIH HHS · UH3 AI083263 · United States
NIDDK NIH HHS · UH2DK083990 · United States
NHGRI NIH HHS · U54HG004968 · United States
NHGRI NIH HHS · R01 HG004906 · United States
NHGRI NIH HHS · R01HG005969 · United States
NHGRI NIH HHS · R01 HG004877 · United States
NIDCR NIH HHS · P30 DE020751 · United States
NHGRI NIH HHS · R01 HG005172 · United States
NIAMS NIH HHS · UH2AR057506 · United States
Corrections
CommentIn
PMID: 22699602
External Links
PubMed source DOI: 10.1038/nature11209 PMC Full Text View journal details
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