Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower; Dirk Gevers; Rob Knight; Sahar Abubucker; Jonathan H. Badger; Asif T. Chinwalla; Heather H. Creasy; Ashlee M. Earl; Michael G. Fitzgerald; Robert S. Fulton; Michelle G. Giglio; Kymberlie Hallsworth-Pepin; Elizabeth A. Lobos; Ramana Madupu; Vincent Magrini; John C. Martin; Makedonka Mitreva; Donna M. Muzny; Erica J. Sodergren; James Versalovic; Aye M. Wollam; Kim C. Worley; Jennifer R. Wortman; Sarah K. Young; Qiandong Zeng; Kjersti M. Aagaard; Olukemi O. Abolude; Emma Allen-Vercoe; Eric J. Alm; Lucia Alvarado; Gary L. Andersen; Scott Anderson; Elizabeth Appelbaum; Harindra M. Arachchi; Gary Armitage; Cesar A. Arze; Tulin Ayvaz; Carl C. Baker; Lisa Begg; Tsegahiwot Belachew; Veena Bhonagiri; Monika Bihan; Martin J. Blaser; Toby Bloom; Vivien Bonazzi; J. Paul Brooks; Gregory A. Buck; Christian J. Buhay; Dana A. Busam; Joseph L. Campbell; Shane R. Canon; Brandi L. Cantarel; Patrick S.G. Chain; I. Min A. Chen; Lei Chen; Shaila Chhibba; Ken Chu; Dawn M. Ciulla; Jose C. Clemente; Sandra W. Clifton; Sean Conlan; Jonathan Crabtree; Mary A. Cutting; Noam J. Davidovics; Catherine C. Davis; Todd Z. Desantis; Carolyn Deal; Kimberley D. Delehaunty; Floyd E. Dewhirst; Elena Deych; Yan Ding; David J. Dooling; Shannon P. Dugan; Wm Michael Dunne; A. Scott Durkin; Robert C. Edgar; Rachel L. Erlich; Candace N. Farmer; Ruth M. Farrell; Karoline Faust; Michael Feldgarden; Victor M. Felix; Sheila Fisher; Anthony A. Fodor; Larry J. Forney; Leslie Foster; Valentina Di Francesco; Jonathan Friedman; Dennis C. Friedrich; Catrina C. Fronick; Lucinda L. Fulton; Hongyu Gao; Nathalia Garcia; Georgia Giannoukos; Christina Giblin; Maria Y. Giovanni; Jonathan M. Goldberg; Johannes Goll; Antonio Gonzalez; Allison Griggs; Sharvari Gujja; Susan Kinder Haake; Brian J. Haas; Holli A. Hamilton; Emily L. Harris; Theresa A. Hepburn; Brandi Herter; Diane E. Hoffmann; Michael E. Holder; Clinton Howarth; Katherine H. Huang; Susan M. Huse; Jacques Izard; Janet K. Jansson; Huaiyang Jiang; Catherine Jordan; Vandita Joshi; James A. Katancik; Wendy A. Keitel; Scott T. Kelley; Cristyn Kells; Nicholas B. King; Dan Knights; Heidi H. Kong; Omry Koren; Sergey Koren; Karthik C. Kota; Christie L. Kovar; Nikos C. Kyrpides; Patricio S. La Rosa; Sandra L. Lee; Katherine P. Lemon; Niall Lennon; Cecil M. Lewis; Lora Lewis; Ruth E. Ley; Kelvin Li; Konstantinos Liolios; Bo Liu; Yue Liu; Chien Chi Lo; Catherine A. Lozupone; R. Dwayne Lunsford; Tessa Madden; Anup A. Mahurkar; Peter J. Mannon; Elaine R. Mardis; Victor M. Markowitz; Konstantinos Mavromatis; Jamison M. McCorrison; Daniel McDonald; Jean McEwen; Amy L. McGuire; Pamela McInnes; Teena Mehta; Kathie A. Mihindukulasuriya; Jason R. Miller; Patrick J. Minx; Irene Newsham; Chad Nusbaum; Michelle Oglaughlin; Joshua Orvis; Ioanna Pagani; Krishna Palaniappan; Shital M. Patel; Matthew Pearson; Jane Peterson; Mircea Podar; Craig Pohl; Katherine S. Pollard; Mihai Pop; Margaret E. Priest; Lita M. Proctor; Xiang Qin; Jeroen Raes; Jacques Ravel; Jeffrey G. Reid; Mina Rho; Rosamond Rhodes; Kevin P. Riehle; Maria C. Rivera; Beltran Rodriguez-Mueller; Yu Hui Rogers; Matthew C. Ross; Carsten Russ; Ravi K. Sanka; Pamela Sankar; J. Fah Sathirapongsasuti; Jeffery A. Schloss; Patrick D. Schloss; Thomas M. Schmidt; Matthew Scholz; Lynn Schriml; Alyxandria M. Schubert; Nicola Segata; Julia A. Segre; William D. Shannon; Richard R. Sharp; Thomas J. Sharpton; Narmada Shenoy; Nihar U. Sheth; Gina A. Simone; Indresh Singh; Christopher S. Smillie; Jack D. Sobel; Daniel D. Sommer; Paul Spicer; Granger G. Sutton; Sean M. Sykes; Diana G. Tabbaa; Mathangi Thiagarajan; Chad M. Tomlinson; Manolito Torralba; Todd J. Treangen; Rebecca M. Truty; Tatiana A. Vishnivetskaya; Jason Walker; Lu Wang; Zhengyuan Wang; Doyle V. Ward; Wesley Warren; Mark A. Watson; Christopher Wellington; Kris A. Wetterstrand; James R. White; Katarzyna Wilczek-Boney; Yuanqing Wu; Kristine M. Wylie; Todd Wylie; Chandri Yandava; Liang Ye; Yuzhen Ye; Shibu Yooseph; Bonnie P. Youmans; Lan Zhang; Yanjiao Zhou; Yiming Zhu; Laurie Zoloth; Jeremy D. Zucker; Bruce W. Birren; Richard A. Gibbs; Sarah K. Highlander; Barbara A. Methé; Karen E. Nelson; Joseph F. Petrosino; George M. Weinstock; Richard K. Wilson; Owen White

doi:10.1038/nature11234

Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower^*, Dirk Gevers, Rob Knight, Sahar Abubucker, Jonathan H. Badger, Asif T. Chinwalla, Heather H. Creasy, Ashlee M. Earl, Michael G. Fitzgerald, Robert S. Fulton, Michelle G. Giglio, Kymberlie Hallsworth-Pepin, Elizabeth A. Lobos, Ramana Madupu, Vincent Magrini, John C. Martin, Makedonka Mitreva, Donna M. Muzny, Erica J. Sodergren, James VersalovicAye M. Wollam, Kim C. Worley, Jennifer R. Wortman, Sarah K. Young, Qiandong Zeng, Kjersti M. Aagaard, Olukemi O. Abolude, Emma Allen-Vercoe, Eric J. Alm, Lucia Alvarado, Gary L. Andersen, Scott Anderson, Elizabeth Appelbaum, Harindra M. Arachchi, Gary Armitage, Cesar A. Arze, Tulin Ayvaz, Carl C. Baker, Lisa Begg, Tsegahiwot Belachew, Veena Bhonagiri, Monika Bihan, Martin J. Blaser, Toby Bloom, Vivien Bonazzi, J. Paul Brooks, Gregory A. Buck, Christian J. Buhay, Dana A. Busam, Joseph L. Campbell, Shane R. Canon, Brandi L. Cantarel, Patrick S.G. Chain, I. Min A. Chen, Lei Chen, Shaila Chhibba, Ken Chu, Dawn M. Ciulla, Jose C. Clemente, Sandra W. Clifton, Sean Conlan, Jonathan Crabtree, Mary A. Cutting, Noam J. Davidovics, Catherine C. Davis, Todd Z. Desantis, Carolyn Deal, Kimberley D. Delehaunty, Floyd E. Dewhirst, Elena Deych, Yan Ding, David J. Dooling, Shannon P. Dugan, Wm Michael Dunne, A. Scott Durkin, Robert C. Edgar, Rachel L. Erlich, Candace N. Farmer, Ruth M. Farrell, Karoline Faust, Michael Feldgarden, Victor M. Felix, Sheila Fisher, Anthony A. Fodor, Larry J. Forney, Leslie Foster, Valentina Di Francesco, Jonathan Friedman, Dennis C. Friedrich, Catrina C. Fronick, Lucinda L. Fulton, Hongyu Gao, Nathalia Garcia, Georgia Giannoukos, Christina Giblin, Maria Y. Giovanni, Jonathan M. Goldberg, Johannes Goll, Antonio Gonzalez, Allison Griggs, Sharvari Gujja, Susan Kinder Haake, Brian J. Haas, Holli A. Hamilton, Emily L. Harris, Theresa A. Hepburn, Brandi Herter, Diane E. Hoffmann, Michael E. Holder, Clinton Howarth, Katherine H. Huang, Susan M. Huse, Jacques Izard, Janet K. Jansson, Huaiyang Jiang, Catherine Jordan, Vandita Joshi, James A. Katancik, Wendy A. Keitel, Scott T. Kelley, Cristyn Kells, Nicholas B. King, Dan Knights, Heidi H. Kong, Omry Koren, Sergey Koren, Karthik C. Kota, Christie L. Kovar, Nikos C. Kyrpides, Patricio S. La Rosa, Sandra L. Lee, Katherine P. Lemon, Niall Lennon, Cecil M. Lewis, Lora Lewis, Ruth E. Ley, Kelvin Li, Konstantinos Liolios, Bo Liu, Yue Liu, Chien Chi Lo, Catherine A. Lozupone, R. Dwayne Lunsford, Tessa Madden, Anup A. Mahurkar, Peter J. Mannon, Elaine R. Mardis, Victor M. Markowitz, Konstantinos Mavromatis, Jamison M. McCorrison, Daniel McDonald, Jean McEwen, Amy L. McGuire, Pamela McInnes, Teena Mehta, Kathie A. Mihindukulasuriya, Jason R. Miller, Patrick J. Minx, Irene Newsham, Chad Nusbaum, Michelle Oglaughlin, Joshua Orvis, Ioanna Pagani, Krishna Palaniappan, Shital M. Patel, Matthew Pearson, Jane Peterson, Mircea Podar, Craig Pohl, Katherine S. Pollard, Mihai Pop, Margaret E. Priest, Lita M. Proctor, Xiang Qin, Jeroen Raes, Jacques Ravel, Jeffrey G. Reid, Mina Rho, Rosamond Rhodes, Kevin P. Riehle, Maria C. Rivera, Beltran Rodriguez-Mueller, Yu Hui Rogers, Matthew C. Ross, Carsten Russ, Ravi K. Sanka, Pamela Sankar, J. Fah Sathirapongsasuti, Jeffery A. Schloss, Patrick D. Schloss, Thomas M. Schmidt, Matthew Scholz, Lynn Schriml, Alyxandria M. Schubert, Nicola Segata, Julia A. Segre, William D. Shannon, Richard R. Sharp, Thomas J. Sharpton, Narmada Shenoy, Nihar U. Sheth, Gina A. Simone, Indresh Singh, Christopher S. Smillie, Jack D. Sobel, Daniel D. Sommer, Paul Spicer, Granger G. Sutton, Sean M. Sykes, Diana G. Tabbaa, Mathangi Thiagarajan, Chad M. Tomlinson, Manolito Torralba, Todd J. Treangen, Rebecca M. Truty, Tatiana A. Vishnivetskaya, Jason Walker, Lu Wang, Zhengyuan Wang, Doyle V. Ward, Wesley Warren, Mark A. Watson, Christopher Wellington, Kris A. Wetterstrand, James R. White, Katarzyna Wilczek-Boney, Yuanqing Wu, Kristine M. Wylie, Todd Wylie, Chandri Yandava, Liang Ye, Yuzhen Ye, Shibu Yooseph, Bonnie P. Youmans, Lan Zhang, Yanjiao Zhou, Yiming Zhu, Laurie Zoloth, Jeremy D. Zucker, Bruce W. Birren, Richard A. Gibbs, Sarah K. Highlander, Barbara A. Methé, Karen E. Nelson, Joseph F. Petrosino, George M. Weinstock, Richard K. Wilson, Owen White

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

8370 Scopus citations

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	https://doi.org/10.1038/nature11234
State	Published - 14 Jun 2012
Externally published	Yes

Access to Document

10.1038/nature11234

Cite this

Huttenhower, C., Gevers, D., Knight, R., Abubucker, S., Badger, J. H., Chinwalla, A. T., Creasy, H. H., Earl, A. M., Fitzgerald, M. G., Fulton, R. S., Giglio, M. G., Hallsworth-Pepin, K., Lobos, E. A., Madupu, R., Magrini, V., Martin, J. C., Mitreva, M., Muzny, D. M., Sodergren, E. J., ... White, O. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207-214. https://doi.org/10.1038/nature11234

@article{6b033f3a80044b7dab151c7770262ad7,

title = "Structure, function and diversity of the healthy human microbiome",

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.",

author = "Curtis Huttenhower and Dirk Gevers and Rob Knight and Sahar Abubucker and Badger, {Jonathan H.} and Chinwalla, {Asif T.} and Creasy, {Heather H.} and Earl, {Ashlee M.} and Fitzgerald, {Michael G.} and Fulton, {Robert S.} and Giglio, {Michelle G.} and Kymberlie Hallsworth-Pepin and Lobos, {Elizabeth A.} and Ramana Madupu and Vincent Magrini and Martin, {John C.} and Makedonka Mitreva and Muzny, {Donna M.} and Sodergren, {Erica J.} and James Versalovic and Wollam, {Aye M.} and Worley, {Kim C.} and Wortman, {Jennifer R.} and Young, {Sarah K.} and Qiandong Zeng and Aagaard, {Kjersti M.} and Abolude, {Olukemi O.} and Emma Allen-Vercoe and Alm, {Eric J.} and Lucia Alvarado and Andersen, {Gary L.} and Scott Anderson and Elizabeth Appelbaum and Arachchi, {Harindra M.} and Gary Armitage and Arze, {Cesar A.} and Tulin Ayvaz and Baker, {Carl C.} and Lisa Begg and Tsegahiwot Belachew and Veena Bhonagiri and Monika Bihan and Blaser, {Martin J.} and Toby Bloom and Vivien Bonazzi and {Paul Brooks}, J. and Buck, {Gregory A.} and Buhay, {Christian J.} and Busam, {Dana A.} and Campbell, {Joseph L.} and Canon, {Shane R.} and Cantarel, {Brandi L.} and Chain, {Patrick S.G.} and Chen, {I. Min A.} and Lei Chen and Shaila Chhibba and Ken Chu and Ciulla, {Dawn M.} and Clemente, {Jose C.} and Clifton, {Sandra W.} and Sean Conlan and Jonathan Crabtree and Cutting, {Mary A.} and Davidovics, {Noam J.} and Davis, {Catherine C.} and Desantis, {Todd Z.} and Carolyn Deal and Delehaunty, {Kimberley D.} and Dewhirst, {Floyd E.} and Elena Deych and Yan Ding and Dooling, {David J.} and Dugan, {Shannon P.} and {Michael Dunne}, Wm and {Scott Durkin}, A. and Edgar, {Robert C.} and Erlich, {Rachel L.} and Farmer, {Candace N.} and Farrell, {Ruth M.} and Karoline Faust and Michael Feldgarden and Felix, {Victor M.} and Sheila Fisher and Fodor, {Anthony A.} and Forney, {Larry J.} and Leslie Foster and {Di Francesco}, Valentina and Jonathan Friedman and Friedrich, {Dennis C.} and Fronick, {Catrina C.} and Fulton, {Lucinda L.} and Hongyu Gao and Nathalia Garcia and Georgia Giannoukos and Christina Giblin and Giovanni, {Maria Y.} and Goldberg, {Jonathan M.} and Johannes Goll and Antonio Gonzalez and Allison Griggs and Sharvari Gujja and {Kinder Haake}, Susan and Haas, {Brian J.} and Hamilton, {Holli A.} and Harris, {Emily L.} and Hepburn, {Theresa A.} and Brandi Herter and Hoffmann, {Diane E.} and Holder, {Michael E.} and Clinton Howarth and Huang, {Katherine H.} and Huse, {Susan M.} and Jacques Izard and Jansson, {Janet K.} and Huaiyang Jiang and Catherine Jordan and Vandita Joshi and Katancik, {James A.} and Keitel, {Wendy A.} and Kelley, {Scott T.} and Cristyn Kells and King, {Nicholas B.} and Dan Knights and Kong, {Heidi H.} and Omry Koren and Sergey Koren and Kota, {Karthik C.} and Kovar, {Christie L.} and Kyrpides, {Nikos C.} and {La Rosa}, {Patricio S.} and Lee, {Sandra L.} and Lemon, {Katherine P.} and Niall Lennon and Lewis, {Cecil M.} and Lora Lewis and Ley, {Ruth E.} and Kelvin Li and Konstantinos Liolios and Bo Liu and Yue Liu and Lo, {Chien Chi} and Lozupone, {Catherine A.} and {Dwayne Lunsford}, R. and Tessa Madden and Mahurkar, {Anup A.} and Mannon, {Peter J.} and Mardis, {Elaine R.} and Markowitz, {Victor M.} and Konstantinos Mavromatis and McCorrison, {Jamison M.} and Daniel McDonald and Jean McEwen and McGuire, {Amy L.} and Pamela McInnes and Teena Mehta and Mihindukulasuriya, {Kathie A.} and Miller, {Jason R.} and Minx, {Patrick J.} and Irene Newsham and Chad Nusbaum and Michelle Oglaughlin and Joshua Orvis and Ioanna Pagani and Krishna Palaniappan and Patel, {Shital M.} and Matthew Pearson and Jane Peterson and Mircea Podar and Craig Pohl and Pollard, {Katherine S.} and Mihai Pop and Priest, {Margaret E.} and Proctor, {Lita M.} and Xiang Qin and Jeroen Raes and Jacques Ravel and Reid, {Jeffrey G.} and Mina Rho and Rosamond Rhodes and Riehle, {Kevin P.} and Rivera, {Maria C.} and Beltran Rodriguez-Mueller and Rogers, {Yu Hui} and Ross, {Matthew C.} and Carsten Russ and Sanka, {Ravi K.} and Pamela Sankar and {Fah Sathirapongsasuti}, J. and Schloss, {Jeffery A.} and Schloss, {Patrick D.} and Schmidt, {Thomas M.} and Matthew Scholz and Lynn Schriml and Schubert, {Alyxandria M.} and Nicola Segata and Segre, {Julia A.} and Shannon, {William D.} and Sharp, {Richard R.} and Sharpton, {Thomas J.} and Narmada Shenoy and Sheth, {Nihar U.} and Simone, {Gina A.} and Indresh Singh and Smillie, {Christopher S.} and Sobel, {Jack D.} and Sommer, {Daniel D.} and Paul Spicer and Sutton, {Granger G.} and Sykes, {Sean M.} and Tabbaa, {Diana G.} and Mathangi Thiagarajan and Tomlinson, {Chad M.} and Manolito Torralba and Treangen, {Todd J.} and Truty, {Rebecca M.} and Vishnivetskaya, {Tatiana A.} and Jason Walker and Lu Wang and Zhengyuan Wang and Ward, {Doyle V.} and Wesley Warren and Watson, {Mark A.} and Christopher Wellington and Wetterstrand, {Kris A.} and White, {James R.} and Katarzyna Wilczek-Boney and Yuanqing Wu and Wylie, {Kristine M.} and Todd Wylie and Chandri Yandava and Liang Ye and Yuzhen Ye and Shibu Yooseph and Youmans, {Bonnie P.} and Lan Zhang and Yanjiao Zhou and Yiming Zhu and Laurie Zoloth and Zucker, {Jeremy D.} and Birren, {Bruce W.} and Gibbs, {Richard A.} and Highlander, {Sarah K.} and Meth{\'e}, {Barbara A.} and Nelson, {Karen E.} and Petrosino, {Joseph F.} and Weinstock, {George M.} and Wilson, {Richard K.} and Owen White",

note = "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{\textquoteright}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.",

year = "2012",

month = jun,

day = "14",

doi = "10.1038/nature11234",

language = "English",

volume = "486",

pages = "207--214",

journal = "Nature",

issn = "0028-0836",

number = "7402",

}

Huttenhower, C, Gevers, D, Knight, R, Abubucker, S, Badger, JH, Chinwalla, AT, Creasy, HH, Earl, AM, Fitzgerald, MG, Fulton, RS, Giglio, MG, Hallsworth-Pepin, K, Lobos, EA, Madupu, R, Magrini, V, Martin, JC, Mitreva, M, Muzny, DM, Sodergren, EJ, Versalovic, J, Wollam, AM, Worley, KC, Wortman, JR, Young, SK, Zeng, Q, Aagaard, KM, Abolude, OO, Allen-Vercoe, E, Alm, EJ, Alvarado, L, Andersen, GL, Anderson, S, Appelbaum, E, Arachchi, HM, Armitage, G, Arze, CA, Ayvaz, T, Baker, CC, Begg, L, Belachew, T, Bhonagiri, V, Bihan, M, Blaser, MJ, Bloom, T, Bonazzi, V, Paul Brooks, J, Buck, GA, Buhay, CJ, Busam, DA, Campbell, JL, Canon, SR, Cantarel, BL, Chain, PSG, Chen, IMA, Chen, L, Chhibba, S, Chu, K, Ciulla, DM, Clemente, JC, Clifton, SW, Conlan, S, Crabtree, J, Cutting, MA, Davidovics, NJ, Davis, CC, Desantis, TZ, Deal, C, Delehaunty, KD, Dewhirst, FE, Deych, E, Ding, Y, Dooling, DJ, Dugan, SP, Michael Dunne, W, Scott Durkin, A, Edgar, RC, Erlich, RL, Farmer, CN, Farrell, RM, Faust, K, Feldgarden, M, Felix, VM, Fisher, S, Fodor, AA, Forney, LJ, Foster, L, Di Francesco, V, Friedman, J, Friedrich, DC, Fronick, CC, Fulton, LL, Gao, H, Garcia, N, Giannoukos, G, Giblin, C, Giovanni, MY, Goldberg, JM, Goll, J, Gonzalez, A, Griggs, A, Gujja, S, Kinder Haake, S, Haas, BJ, Hamilton, HA, Harris, EL, Hepburn, TA, Herter, B, Hoffmann, DE, Holder, ME, Howarth, C, Huang, KH, Huse, SM, Izard, J, Jansson, JK, Jiang, H, Jordan, C, Joshi, V, Katancik, JA, Keitel, WA, Kelley, ST, Kells, C, King, NB, Knights, D, Kong, HH, Koren, O, Koren, S, Kota, KC, Kovar, CL, Kyrpides, NC, La Rosa, PS, Lee, SL, Lemon, KP, Lennon, N, Lewis, CM, Lewis, L, Ley, RE, Li, K, Liolios, K, Liu, B, Liu, Y, Lo, CC, Lozupone, CA, Dwayne Lunsford, R, Madden, T, Mahurkar, AA, Mannon, PJ, Mardis, ER, Markowitz, VM, Mavromatis, K, McCorrison, JM, McDonald, D, McEwen, J, McGuire, AL, McInnes, P, Mehta, T, Mihindukulasuriya, KA, Miller, JR, Minx, PJ, Newsham, I, Nusbaum, C, Oglaughlin, M, Orvis, J, Pagani, I, Palaniappan, K, Patel, SM, Pearson, M, Peterson, J, Podar, M, Pohl, C, Pollard, KS, Pop, M, Priest, ME, Proctor, LM, Qin, X, Raes, J, Ravel, J, Reid, JG, Rho, M, Rhodes, R, Riehle, KP, Rivera, MC, Rodriguez-Mueller, B, Rogers, YH, Ross, MC, Russ, C, Sanka, RK, Sankar, P, Fah Sathirapongsasuti, J, Schloss, JA, Schloss, PD, Schmidt, TM, Scholz, M, Schriml, L, Schubert, AM, Segata, N, Segre, JA, Shannon, WD, Sharp, RR, Sharpton, TJ, Shenoy, N, Sheth, NU, Simone, GA, Singh, I, Smillie, CS, Sobel, JD, Sommer, DD, Spicer, P, Sutton, GG, Sykes, SM, Tabbaa, DG, Thiagarajan, M, Tomlinson, CM, Torralba, M, Treangen, TJ, Truty, RM, Vishnivetskaya, TA, Walker, J, Wang, L, Wang, Z, Ward, DV, Warren, W, Watson, MA, Wellington, C, Wetterstrand, KA, White, JR, Wilczek-Boney, K, Wu, Y, Wylie, KM, Wylie, T, Yandava, C, Ye, L, Ye, Y, Yooseph, S, Youmans, BP, Zhang, L, Zhou, Y, Zhu, Y, Zoloth, L, Zucker, JD, Birren, BW, Gibbs, RA, Highlander, SK, Methé, BA, Nelson, KE, Petrosino, JF, Weinstock, GM, Wilson, RK & White, O 2012, 'Structure, function and diversity of the healthy human microbiome', Nature, vol. 486, no. 7402, pp. 207-214. https://doi.org/10.1038/nature11234

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.

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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 -

Structure, function and diversity of the healthy human microbiome

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