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.
Original language | English |
---|---|
Pages (from-to) | 207-214 |
Number of pages | 8 |
Journal | Nature |
Volume | 486 |
Issue number | 7402 |
DOIs | |
State | Published - Jun 14 2012 |
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In: Nature, Vol. 486, No. 7402, 14.06.2012, p. 207-214.
Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - Structure, function and diversity of the healthy human microbiome
AU - Huttenhower, Curtis
AU - Gevers, Dirk
AU - Knight, Rob
AU - Abubucker, Sahar
AU - Badger, Jonathan H.
AU - Chinwalla, Asif T.
AU - Creasy, Heather H.
AU - Earl, Ashlee M.
AU - Fitzgerald, Michael G.
AU - Fulton, Robert S.
AU - Giglio, Michelle G.
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
AU - Paul Brooks, J.
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.G.
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, Wm
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 J.
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 - Kinder Haake, Susan
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 - King, Nicholas B.
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 - Mavromatis, 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 - Oglaughlin, 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 - Pop, Mihai
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, Christopher 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 - Wu, Yuanqing
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 - Methé, Barbara A.
AU - Nelson, Karen E.
AU - Petrosino, Joseph F.
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 National Center for Biotechnology Information and the Intramural Research Program of the NIH National Library of Medicine. We appreciate the participation of the individuals from the Saint Louis, Missouri, and Houston, Texas areas who made this study possible. This research was supported in part by National Institutes of Health 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.R.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.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); 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 RC1DE0202098 and 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. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon& Betty Moore Foundationfunding and institutionalfunding 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 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84862276328&partnerID=8YFLogxK
U2 - 10.1038/nature11234
DO - 10.1038/nature11234
M3 - Article
C2 - 22699609
AN - SCOPUS:84862276328
SN - 0028-0836
VL - 486
SP - 207
EP - 214
JO - Nature
JF - Nature
IS - 7402
ER -