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.
Original language | English (US) |
---|---|
Pages (from-to) | 215-221 |
Number of pages | 7 |
Journal | Nature |
Volume | 486 |
Issue number | 7402 |
DOIs | |
State | Published - Jun 14 2012 |
ASJC Scopus subject areas
- General
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In: Nature, Vol. 486, No. 7402, 14.06.2012, p. 215-221.
Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - A framework for human microbiome research
AU - Methé, Barbara A.
AU - Nelson, Karen E.
AU - Pop, Mihai
AU - Creasy, Heather H.
AU - Giglio, Michelle G.
AU - Huttenhower, Curtis
AU - Gevers, Dirk
AU - Petrosino, Joseph F.
AU - Abubucker, Sahar
AU - Badger, Jonathan H.
AU - Chinwalla, Asif T.
AU - Earl, Ashlee M.
AU - Fitzgerald, Michael G.
AU - Fulton, Robert S.
AU - Hallsworth-Pepin, Kymberlie
AU - Lobos, Elizabeth A.
AU - Madupu, Ramana
AU - Magrini, Vincent
AU - Martin, John C.
AU - Mitreva, Makedonka
AU - Muzny, Donna M.
AU - Sodergren, Erica J.
AU - Versalovic, James
AU - Wollam, Aye M.
AU - Worley, Kim C.
AU - Wortman, Jennifer R.
AU - Young, Sarah K.
AU - Zeng, Qiandong
AU - Aagaard, Kjersti M.
AU - Abolude, Olukemi O.
AU - Allen-Vercoe, Emma
AU - Alm, Eric J.
AU - Alvarado, Lucia
AU - Andersen, Gary L.
AU - Anderson, Scott
AU - Appelbaum, Elizabeth
AU - Arachchi, Harindra M.
AU - Armitage, Gary
AU - Arze, Cesar A.
AU - Ayvaz, Tulin
AU - Baker, Carl C.
AU - Begg, Lisa
AU - Belachew, Tsegahiwot
AU - Bhonagiri, Veena
AU - Bihan, Monika
AU - Blaser, Martin J.
AU - Bloom, Toby
AU - Bonazzi, Vivien R.
AU - Brooks, Paul
AU - Buck, Gregory A.
AU - Buhay, Christian J.
AU - Busam, Dana A.
AU - Campbell, Joseph L.
AU - Canon, Shane R.
AU - Cantarel, Brandi L.
AU - Chain, Patrick S.
AU - Chen, I. Min A
AU - Chen, Lei
AU - Chhibba, Shaila
AU - Chu, Ken
AU - Ciulla, Dawn M.
AU - Clemente, Jose C.
AU - Clifton, Sandra W.
AU - Conlan, Sean
AU - Crabtree, Jonathan
AU - Cutting, Mary A.
AU - Davidovics, Noam J.
AU - Davis, Catherine C.
AU - Desantis, Todd Z.
AU - Deal, Carolyn
AU - Delehaunty, Kimberley D.
AU - Dewhirst, Floyd E.
AU - Deych, Elena
AU - Ding, Yan
AU - Dooling, David J.
AU - Dugan, Shannon P.
AU - Michael Dunne, W.
AU - Scott Durkin, A.
AU - Edgar, Robert C.
AU - Erlich, Rachel L.
AU - Farmer, Candace N.
AU - Farrell, Ruth M.
AU - Faust, Karoline
AU - Feldgarden, Michael
AU - Felix, Victor M.
AU - Fisher, Sheila
AU - Fodor, Anthony A.
AU - Forney, Larry
AU - Foster, Leslie
AU - Di Francesco, Valentina
AU - Friedman, Jonathan
AU - Friedrich, Dennis C.
AU - Fronick, Catrina C.
AU - Fulton, Lucinda L.
AU - Gao, Hongyu
AU - Garcia, Nathalia
AU - Giannoukos, Georgia
AU - Giblin, Christina
AU - Giovanni, Maria Y.
AU - Goldberg, Jonathan M.
AU - Goll, Johannes
AU - Gonzalez, Antonio
AU - Griggs, Allison
AU - Gujja, Sharvari
AU - Haas, Brian J.
AU - Hamilton, Holli A.
AU - Harris, Emily L.
AU - Hepburn, Theresa A.
AU - Herter, Brandi
AU - Hoffmann, Diane E.
AU - Holder, Michael E.
AU - Howarth, Clinton
AU - Huang, Katherine H.
AU - Huse, Susan M.
AU - Izard, Jacques
AU - Jansson, Janet K.
AU - Jiang, Huaiyang
AU - Jordan, Catherine
AU - Joshi, Vandita
AU - Katancik, James A.
AU - Keitel, Wendy A.
AU - Kelley, Scott T.
AU - Kells, Cristyn
AU - Kinder-Haake, Susan
AU - King, Nicholas B.
AU - Knight, Rob
AU - Knights, Dan
AU - Kong, Heidi H.
AU - Koren, Omry
AU - Koren, Sergey
AU - Kota, Karthik C.
AU - Kovar, Christie L.
AU - Kyrpides, Nikos C.
AU - La Rosa, Patricio S.
AU - Lee, Sandra L.
AU - Lemon, Katherine P.
AU - Lennon, Niall
AU - Lewis, Cecil M.
AU - Lewis, Lora
AU - Ley, Ruth E.
AU - Li, Kelvin
AU - Liolios, Konstantinos
AU - Liu, Bo
AU - Liu, Yue
AU - Lo, Chien Chi
AU - Lozupone, Catherine A.
AU - Dwayne Lunsford, R.
AU - Madden, Tessa
AU - Mahurkar, Anup A.
AU - Mannon, Peter J.
AU - Mardis, Elaine R.
AU - Markowitz, Victor M.
AU - Mavrommatis, Konstantinos
AU - McCorrison, Jamison M.
AU - McDonald, Daniel
AU - McEwen, Jean
AU - McGuire, Amy L.
AU - McInnes, Pamela
AU - Mehta, Teena
AU - Mihindukulasuriya, Kathie A.
AU - Miller, Jason R.
AU - Minx, Patrick J.
AU - Newsham, Irene
AU - Nusbaum, Chad
AU - O'Laughlin, Michelle
AU - Orvis, Joshua
AU - Pagani, Ioanna
AU - Palaniappan, Krishna
AU - Patel, Shital M.
AU - Pearson, Matthew
AU - Peterson, Jane
AU - Podar, Mircea
AU - Pohl, Craig
AU - Pollard, Katherine S.
AU - Priest, Margaret E.
AU - Proctor, Lita M.
AU - Qin, Xiang
AU - Raes, Jeroen
AU - Ravel, Jacques
AU - Reid, Jeffrey G.
AU - Rho, Mina
AU - Rhodes, Rosamond
AU - Riehle, Kevin P.
AU - Rivera, Maria C.
AU - Rodriguez-Mueller, Beltran
AU - Rogers, Yu Hui
AU - Ross, Matthew C.
AU - Russ, Carsten
AU - Sanka, Ravi K.
AU - Sankar, Pamela
AU - Fah Sathirapongsasuti, J.
AU - Schloss, Jeffery A.
AU - Schloss, Patrick D.
AU - Schmidt, Thomas M.
AU - Scholz, Matthew
AU - Schriml, Lynn
AU - Schubert, Alyxandria M.
AU - Segata, Nicola
AU - Segre, Julia A.
AU - Shannon, William D.
AU - Sharp, Richard R.
AU - Sharpton, Thomas J.
AU - Shenoy, Narmada
AU - Sheth, Nihar U.
AU - Simone, Gina A.
AU - Singh, Indresh
AU - Smillie, Chris S.
AU - Sobel, Jack D.
AU - Sommer, Daniel D.
AU - Spicer, Paul
AU - Sutton, Granger G.
AU - Sykes, Sean M.
AU - Tabbaa, Diana G.
AU - Thiagarajan, Mathangi
AU - Tomlinson, Chad M.
AU - Torralba, Manolito
AU - Treangen, Todd J.
AU - Truty, Rebecca M.
AU - Vishnivetskaya, Tatiana A.
AU - Walker, Jason
AU - Wang, Lu
AU - Wang, Zhengyuan
AU - Ward, Doyle V.
AU - Warren, Wesley
AU - Watson, Mark A.
AU - Wellington, Christopher
AU - Wetterstrand, Kris A.
AU - White, James R.
AU - Wilczek-Boney, Katarzyna
AU - Qing Wu, Yuan
AU - Wylie, Kristine M.
AU - Wylie, Todd
AU - Yandava, Chandri
AU - Ye, Liang
AU - Ye, Yuzhen
AU - Yooseph, Shibu
AU - Youmans, Bonnie P.
AU - Zhang, Lan
AU - Zhou, Yanjiao
AU - Zhu, Yiming
AU - Zoloth, Laurie
AU - Zucker, Jeremy D.
AU - Birren, Bruce W.
AU - Gibbs, Richard A.
AU - Highlander, Sarah K.
AU - Weinstock, George M.
AU - Wilson, Richard K.
AU - White, Owen
N1 - Funding Information: Acknowledgements The consortium would like to thank our external scientific advisory board: R. Blumberg, J. Davies, R. Holt, P. Ossorio, F. Ouellette, G. Schoolnik and A. Williamson. We would also like to thank our collaborators throughout the International Human Microbiome Consortium, particularly the investigators of the MetaHIT project, for advancing human microbiome research. Data repository management was provided by the NCBI and the Intramural Research Program of the NIH National Library of Medicine. We especially appreciate the generous participation of the individuals from the St Louis, Missouri, and Houston, Texas areas who made this study possible. This research was supported in part by NIH grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E. S. Lander.; U54AI084844 to K.E.N.; N01AI30071 to R. L. Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M. K. Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.M.F.; R01HG005172 to P. Spicer; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.-V.; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); M.J.B. was supported by UH2AR057506, S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T.M.S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J.V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.-H. was supported by RC1DE020298and R01DE021574 (S.K.-H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231 for P.S.C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. andJ. Raes; R.K. is a Howard Hughes Medical Institute (HHMI) Early Career Scientist; Gordon & Betty Moore Foundation funding and institutional funding from the J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.-V.; 2010 IBM Faculty Award to K.C.W. Analysis of the HMP data was performed using National Energy Research Scientific Computing resources; the BluBioU Computational Resource at Rice University.
PY - 2012/6/14
Y1 - 2012/6/14
N2 - 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.
AB - 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.
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U2 - 10.1038/nature11209
DO - 10.1038/nature11209
M3 - Article
C2 - 22699610
AN - SCOPUS:84862286169
SN - 0028-0836
VL - 486
SP - 215
EP - 221
JO - Nature
JF - Nature
IS - 7402
ER -