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 & 228 others 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

Research output: Contribution to journalArticle

3557 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)207-214
Number of pages8
JournalNature
Volume486
Issue number7402
DOIs
StatePublished - Jun 14 2012
Externally publishedYes

Fingerprint

Microbiota
Ecosystem
Ecology
Microbial Genetics
Metagenomics
Vagina
Metabolic Networks and Pathways
Healthy Volunteers
Epidemiology
Diet
Skin
Enzymes
Population

ASJC Scopus subject areas

  • Medicine(all)
  • General

Cite this

Huttenhower, C., Gevers, D., Knight, R., Abubucker, S., Badger, J. H., Chinwalla, A. T., ... White, O. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207-214. https://doi.org/10.1038/nature11234

Structure, function and diversity of the healthy human microbiome. / Huttenhower, Curtis; Gevers, Dirk; Knight, Rob; Abubucker, Sahar; Badger, Jonathan H.; Chinwalla, Asif T.; Creasy, Heather H.; Earl, Ashlee M.; Fitzgerald, Michael G.; Fulton, Robert S.; Giglio, Michelle G.; 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; Paul Brooks, J.; Buck, Gregory A.; Buhay, Christian J.; Busam, Dana A.; Campbell, Joseph L.; Canon, Shane R.; Cantarel, Brandi L.; Chain, Patrick S G; 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.; Michael Dunne, Wm; Scott Durkin, A.; 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 J.; 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; Kinder Haake, Susan; 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; King, Nicholas B.; 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.; Dwayne Lunsford, R.; Madden, Tessa; Mahurkar, Anup A.; Mannon, Peter J.; Mardis, Elaine R.; Markowitz, Victor M.; Mavromatis, 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; Oglaughlin, Michelle; Orvis, Joshua; Pagani, Ioanna; Palaniappan, Krishna; Patel, Shital M.; Pearson, Matthew; Peterson, Jane; Podar, Mircea; Pohl, Craig; Pollard, Katherine S.; Pop, Mihai; 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; Fah Sathirapongsasuti, J.; 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, Christopher 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, Yuanqing; 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.; Methé, Barbara A.; Nelson, Karen E.; Petrosino, Joseph F.; Weinstock, George M.; Wilson, Richard K.; White, Owen.

In: Nature, Vol. 486, No. 7402, 14.06.2012, p. 207-214.

Research output: Contribution to journalArticle

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
Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012 Jun 14;486(7402):207-214. https://doi.org/10.1038/nature11234
Huttenhower, Curtis ; Gevers, Dirk ; Knight, Rob ; Abubucker, Sahar ; Badger, Jonathan H. ; Chinwalla, Asif T. ; Creasy, Heather H. ; Earl, Ashlee M. ; Fitzgerald, Michael G. ; Fulton, Robert S. ; Giglio, Michelle G. ; 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 ; Paul Brooks, J. ; Buck, Gregory A. ; Buhay, Christian J. ; Busam, Dana A. ; Campbell, Joseph L. ; Canon, Shane R. ; Cantarel, Brandi L. ; Chain, Patrick S G ; 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. ; Michael Dunne, Wm ; Scott Durkin, A. ; 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 J. ; 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 ; Kinder Haake, Susan ; 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 ; King, Nicholas B. ; 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. ; Dwayne Lunsford, R. ; Madden, Tessa ; Mahurkar, Anup A. ; Mannon, Peter J. ; Mardis, Elaine R. ; Markowitz, Victor M. ; Mavromatis, 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 ; Oglaughlin, Michelle ; Orvis, Joshua ; Pagani, Ioanna ; Palaniappan, Krishna ; Patel, Shital M. ; Pearson, Matthew ; Peterson, Jane ; Podar, Mircea ; Pohl, Craig ; Pollard, Katherine S. ; Pop, Mihai ; 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 ; Fah Sathirapongsasuti, J. ; 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, Christopher 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, Yuanqing ; 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. ; Methé, Barbara A. ; Nelson, Karen E. ; Petrosino, Joseph F. ; Weinstock, George M. ; Wilson, Richard K. ; White, Owen. / Structure, function and diversity of the healthy human microbiome. In: Nature. 2012 ; Vol. 486, No. 7402. pp. 207-214.
@article{624214cbc79e43c0a7ba0ab0647ad210,
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",
year = "2012",
month = "6",
day = "14",
doi = "10.1038/nature11234",
language = "English (US)",
volume = "486",
pages = "207--214",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7402",

}

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

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

UR - http://www.scopus.com/inward/citedby.url?scp=84862276328&partnerID=8YFLogxK

U2 - 10.1038/nature11234

DO - 10.1038/nature11234

M3 - Article

VL - 486

SP - 207

EP - 214

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7402

ER -