Structure, function and diversity of the healthy human microbiome.
The Human Microbiome Project Consortium *; Huttenhower, Curtis 1,2,81; Gevers, Dirk 2,81; Knight, Rob 3,4; Abubucker, Sahar 5; Badger, Jonathan H. 6; Chinwalla, Asif T. 5; Creasy, Heather H. 7; Earl, Ashlee M. 2; FitzGerald, Michael G. 2; Fulton, Robert S. 5; Giglio, Michelle G. 7; Hallsworth-Pepin, Kymberlie 5; Lobos, Elizabeth A. 5; Madupu, Ramana 6; Magrini, Vincent 5; Martin, John C. 5; Mitreva, Makedonka 5; Muzny, Donna M. 8; Sodergren, Erica J. 5; Versalovic, James 9,10; Wollam, Aye M. 5; Worley, Kim C. 8; Wortman, Jennifer R. 7; Young, Sarah K. 2; Zeng, Qiandong 2; Aagaard, Kjersti M. 11; Abolude, Olukemi O. 7; Allen-Vercoe, Emma 12; Alm, Eric J. 13,2; Alvarado, Lucia 2; Andersen, Gary L. 14; Anderson, Scott 2; Appelbaum, Elizabeth 5; Arachchi, Harindra M. 2; Armitage, Gary 15; Arze, Cesar A. 7; Ayvaz, Tulin 16; Baker, Carl C. 17; Begg, Lisa 18; Belachew, Tsegahiwot 19; Bhonagiri, Veena 5; Bihan, Monika 6; Blaser, Martin J. 20; Bloom, Toby 2; Bonazzi, Vivien 21; Brooks, Paul J. 22,23; Buck, Gregory A. 23,24; Buhay, Christian J. 8; Busam, Dana A. 6; Campbell, Joseph L. 21,19; Canon, Shane R. 25; Cantarel, Brandi L. 7; Chain, Patrick S. G. 26,27; Chen, I-Min A. 28; Chen, Lei 5; Chhibba, Shaila 21; Chu, Ken 28; Ciulla, Dawn M. 2; Clemente, Jose C. 3; Clifton, Sandra W. 5; Conlan, Sean 79; Crabtree, Jonathan 7; Cutting, Mary A. 29; Davidovics, Noam J. 7; Davis, Catherine C. 30; DeSantis, Todd Z. 31; Deal, Carolyn 19; Delehaunty, Kimberley D. 5; Dewhirst, Floyd E. 32,33; Deych, Elena 34; Ding, Yan 8; Dooling, David J. 5; Dugan, Shannon P. 8; Dunne, Wm Michael 35,36; Durkin, Scott A. 6; Edgar, Robert C. 37; Erlich, Rachel L. 2; Farmer, Candace N. 5; Farrell, Ruth M. 38; Faust, Karoline 39,40; Feldgarden, Michael 2; Felix, Victor M. 7; Fisher, Sheila 2; Fodor, Anthony A. 41; Forney, Larry J. 42; Foster, Leslie 6; Di Francesco, Valentina 19; Friedman, Jonathan 43; Friedrich, Dennis C. 2; Fronick, Catrina C. 5; Fulton, Lucinda L. 5; Gao, Hongyu 5; Garcia, Nathalia 44; Giannoukos, Georgia 2; Giblin, Christina 19; Giovanni, Maria Y. 19; Goldberg, Jonathan M. 2; Goll, Johannes 6; Gonzalez, Antonio 45; Griggs, Allison 2; Gujja, Sharvari 2; Haake, Susan Kinder 46; Haas, Brian J. 2; Hamilton, Holli A. 29; Harris, Emily L. 29; Hepburn, Theresa A. 2; Herter, Brandi 5; Hoffmann, Diane E. 47; Holder, Michael E. 8; Howarth, Clinton 2; Huang, Katherine H. 2; Huse, Susan M. 48; Izard, Jacques 32,33; Jansson, Janet K. 49; Jiang, Huaiyang 8; Jordan, Catherine 7; Joshi, Vandita 8; Katancik, James A. 50; Keitel, Wendy A. 16; Kelley, Scott T. 51; Kells, Cristyn 2; King, Nicholas B. 52; Knights, Dan 45; Kong, Heidi H. 53; Koren, Omry 54; Koren, Sergey 55; Kota, Karthik C. 5; Kovar, Christie L. 8; Kyrpides, Nikos C. 27; La Rosa, Patricio S. 34; Lee, Sandra L. 8; Lemon, Katherine P. 32,56; Lennon, Niall 2; Lewis, Cecil M. 57; Lewis, Lora 8; Ley, Ruth E. 54; Li, Kelvin 6; Liolios, Konstantinos 27; Liu, Bo 55; Liu, Yue 8; Lo, Chien-Chi 26; Lozupone, Catherine A. 3; Lunsford, Dwayne R. 29; Madden, Tessa 58; Mahurkar, Anup A. 7; Mannon, Peter J. 59; Mardis, Elaine R. 5; Markowitz, Victor M. 27,28; Mavromatis, Konstantinos 27; McCorrison, Jamison M. 6; McDonald, Daniel 3; McEwen, Jean 21; McGuire, Amy L. 60; McInnes, Pamela 29; Mehta, Teena 2; Mihindukulasuriya, Kathie A. 5; Miller, Jason R. 6; Minx, Patrick J. 5; Newsham, Irene 8; Nusbaum, Chad 2; O'Laughlin, Michelle 5; Orvis, Joshua 7; Pagani, Ioanna 27; Palaniappan, Krishna 28; Patel, Shital M. 61; Pearson, Matthew 2; Peterson, Jane 21; Podar, Mircea 62; Pohl, Craig 5; Pollard, Katherine S. 63,64,65; Pop, Mihai 55,66; Priest, Margaret E. 2; Proctor, Lita M. 21; Qin, Xiang 8; Raes, Jeroen 39,40; Ravel, Jacques 7; Reid, Jeffrey G. 8; Rho, Mina 67; Rhodes, Rosamond 68; Riehle, Kevin P. 69; Rivera, Maria C. 23,24; Rodriguez-Mueller, Beltran 51; Rogers, Yu-Hui 6; Ross, Matthew C. 16; Russ, Carsten 2; Sanka, Ravi K. 6; Sankar, Pamela 70; Sathirapongsasuti, Fah J. 1; Schloss, Jeffery A. 21; Schloss, Patrick D. 71; Schmidt, Thomas M. 72; Scholz, Matthew 26; Schriml, Lynn 7; Schubert, Alyxandria M. 71; Segata, Nicola 1; Segre, Julia A. 79; Shannon, William D. 34; Sharp, Richard R. 38; Sharpton, Thomas J. 63; Shenoy, Narmada 2; Sheth, Nihar U. 23; Simone, Gina A. 73; Singh, Indresh 6; Smillie, Christopher S. 43; Sobel, Jack D. 74; Sommer, Daniel D. 55; Spicer, Paul 57; Sutton, Granger G. 6; Sykes, Sean M. 2; Tabbaa, Diana G. 2; Thiagarajan, Mathangi 6; Tomlinson, Chad M. 5; Torralba, Manolito 6; Treangen, Todd J. 75; Truty, Rebecca M. 63; Vishnivetskaya, Tatiana A. 62; Walker, Jason 5; Wang, Lu 21; Wang, Zhengyuan 5; Ward, Doyle V. 2; Warren, Wesley 5; Watson, Mark A. 35; Wellington, Christopher 21; Wetterstrand, Kris A. 21; White, James R. 7; Wilczek-Boney, Katarzyna 8; Wu, YuanQing 8; Wylie, Kristine M. 5; Wylie, Todd 5; Yandava, Chandri 2; Ye, Liang 5; Ye, Yuzhen 67; Yooseph, Shibu 76; Youmans, Bonnie P. 16; Zhang, Lan 8; Zhou, Yanjiao 5; Zhu, Yiming 8; Zoloth, Laurie 77; Zucker, Jeremy D. 2; Birren, Bruce W. 2; Gibbs, Richard A. 8; Highlander, Sarah K. 8,16; Methe, Barbara A. 6; Nelson, Karen E. 6; Petrosino, Joseph F. 8,78,16; Weinstock, George M. 5; Wilson, Richard K. 5; White, Owen 7
[Article]
Nature.
486(7402):207-214, June 14, 2012.
(Format: HTML, PDF)
: 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.
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