A framework for human microbiome research.
The Human Microbiome Project Consortium *; Methe, Barbara A. 1; Nelson, Karen E. 1; Pop, Mihai 2; Creasy, Heather H. 3; Giglio, Michelle G. 3; Huttenhower, Curtis 4,5; Gevers, Dirk 5; Petrosino, Joseph F. 6,15,79; Abubucker, Sahar 7; Badger, Jonathan H. 77; Chinwalla, Asif T. 7; Earl, Ashlee M. 5; FitzGerald, Michael G. 5; Fulton, Robert S. 7; Hallsworth-Pepin, Kymberlie 7; Lobos, Elizabeth A. 7; Madupu, Ramana 1; Magrini, Vincent 7; Martin, John C. 7; Mitreva, Makedonka 7; Muzny, Donna M. 6; Sodergren, Erica J. 7; Versalovic, James 8,9; Wollam, Aye M. 7; Worley, Kim C. 6; Wortman, Jennifer R. 5; Young, Sarah K. 5; Zeng, Qiandong 5; Aagaard, Kjersti M. 10; Abolude, Olukemi O. 3; Allen-Vercoe, Emma 11; Alm, Eric J. 5,12; Alvarado, Lucia 5; Andersen, Gary L. 13; Anderson, Scott 5; Appelbaum, Elizabeth 7; Arachchi, Harindra M. 5; Armitage, Gary 14; Arze, Cesar A. 3; Ayvaz, Tulin 15; Baker, Carl C. 16; Begg, Lisa 17; Belachew, Tsegahiwot 18; Bhonagiri, Veena 7; Bihan, Monika 1; Blaser, Martin J. 19; Bloom, Toby 5; Bonazzi, Vivien R. 20; Brooks, Paul 21,22; Buck, Gregory A. 22,23; Buhay, Christian J. 6; Busam, Dana A. 1; Campbell, Joseph L. 18,20; Canon, Shane R. 24; Cantarel, Brandi L. 3; Chain, Patrick S. 25,26; Chen, I-Min A. 27; Chen, Lei 7; Chhibba, Shaila 20; Chu, Ken 27; Ciulla, Dawn M. 5; Clemente, Jose C. 28; Clifton, Sandra W. 7; Conlan, Sean 80; Crabtree, Jonathan 3; Cutting, Mary A. 29; Davidovics, Noam J. 3; Davis, Catherine C. 30; DeSantis, Todd Z. 31; Deal, Carolyn 18; Delehaunty, Kimberley D. 7; Dewhirst, Floyd E. 32,33; Deych, Elena 7; Ding, Yan 6; Dooling, David J. 7; Dugan, Shannon P. 6; Dunne, Michael W. Jr 34,35; Durkin, Scott A. 1; Edgar, Robert C. 36; Erlich, Rachel L. 5; Farmer, Candace N. 7; Farrell, Ruth M. 37; Faust, Karoline 38,39; Feldgarden, Michael 5; Felix, Victor M. 3; Fisher, Sheila 5; Fodor, Anthony A. 40; Forney, Larry 41; Foster, Leslie 1; Di Francesco, Valentina 18; Friedman, Jonathan 42; Friedrich, Dennis C. 5; Fronick, Catrina C. 7; Fulton, Lucinda L. 7; Gao, Hongyu 8; Garcia, Nathalia 43; Giannoukos, Georgia 5; Giblin, Christina 18; Giovanni, Maria Y. 18; Goldberg, Jonathan M. 5; Goll, Johannes 1; Gonzalez, Antonio 44; Griggs, Allison 5; Gujja, Sharvari 5; Haas, Brian J. 5; Hamilton, Holli A. 29; Harris, Emily L. 29; Hepburn, Theresa A. 5; Herter, Brandi 7; Hoffmann, Diane E. 45; Holder, Michael E. 6; Howarth, Clinton 5; Huang, Katherine H. 5; Huse, Susan M. 46; Izard, Jacques 32,33; Jansson, Janet K. 48; Jiang, Huaiyang 6; Jordan, Catherine 3; Joshi, Vandita 6; Katancik, James A. 49; Keitel, Wendy A. 15; Kelley, Scott T. 50; Kells, Cristyn 5; Kinder-Haake, Susan 51,82,; King, Nicholas B. 52; Knight, Rob 28,53; Knights, Dan 44; Kong, Heidi H. 54; Koren, Omry 55; Koren, Sergey 2; Kota, Karthik C. 7; Kovar, Christie L. 6; Kyrpides, Nikos C. 26; La Rosa, Patricio S. 56; Lee, Sandra L. 6; Lemon, Katherine P. 32,57; Lennon, Niall 6; Lewis, Cecil M. 58; Lewis, Lora 6; Ley, Ruth E. 55; Li, Kelvin 1; Liolios, Konstantinos 26; Liu, Bo 2; Liu, Yue 6; Lo, Chien-Chi 25; Lozupone, Catherine A. 28; Lunsford, Dwayne R. 29; Madden, Tessa 59; Mahurkar, Anup A. 3; Mannon, Peter J. 60; Mardis, Elaine R. 7; Markowitz, Victor M. 26,27; Mavrommatis, Konstantinos 26; McCorrison, Jamison M. 1; McDonald, Daniel 28; McEwen, Jean 20; McGuire, Amy L. 61; McInnes, Pamela 29; Mehta, Teena 5; Mihindukulasuriya, Kathie A. 7; Miller, Jason R. 1; Minx, Patrick J. 7; Newsham, Irene 6; Nusbaum, Chad 5; O'Laughlin, Michelle 7; Orvis, Joshua 3; Pagani, Ioanna 26; Palaniappan, Krishna 27; Patel, Shital M. 62; Pearson, Matthew 5; Peterson, Jane 20; Podar, Mircea 63; Pohl, Craig 7; Pollard, Katherine S. 64,65,66; Priest, Margaret E. 5; Proctor, Lita M. 20; Qin, Xiang 6; Raes, Jeroen 38,39; Ravel, Jacques 3,67; Reid, Jeffrey G. 6; Rho, Mina 68; Rhodes, Rosamond 69; Riehle, Kevin P. 70; Rivera, Maria C. 22,23; Rodriguez-Mueller, Beltran 50; Rogers, Yu-Hui 1; Ross, Matthew C. 15; Russ, Carsten 5; Sanka, Ravi K. 1; Sankar, Pamela 71; Sathirapongsasuti, Fah J. 4; Schloss, Jeffery A. 20; Schloss, Patrick D. 72; Schmidt, Thomas M. 73; Scholz, Matthew 25; Schriml, Lynn 3; Schubert, Alyxandria M. 72; Segata, Nicola 4; Segre, Julia A. 80; Shannon, William D. 56; Sharp, Richard R. 37; Sharpton, Thomas J. 64; Shenoy, Narmada 5; Sheth, Nihar U. 22; Simone, Gina A. 74; Singh, Indresh 1; Smillie, Chris S. 42; Sobel, Jack D. 75; Sommer, Daniel D. 2; Spicer, Paul 58; Sutton, Granger G. 1; Sykes, Sean M. 5; Tabbaa, Diana G. 5; Thiagarajan, Mathangi 1; Tomlinson, Chad M. 7; Torralba, Manolito 1; Treangen, Todd J. 76; Truty, Rebecca M. 64; Vishnivetskaya, Tatiana A. 63; Walker, Jason 7; Wang, Lu 20; Wang, Zhengyuan 5; Ward, Doyle V. 5; Warren, Wesley 7; Watson, Mark A. 34; Wellington, Christopher 20; Wetterstrand, Kris A. 20; White, James R. 3; Wilczek-Boney, Katarzyna 6; Wu, Yuan Qing 6; Wylie, Kristine M. 7; Wylie, Todd 7; Yandava, Chandri 5; Ye, Liang 7; Ye, Yuzhen 68; Yooseph, Shibu 77; Youmans, Bonnie P. 15; Zhang, Lan 6; Zhou, Yanjiao 7; Zhu, Yiming 6; Zoloth, Laurie 78; Zucker, Jeremy D. 5; Birren, Bruce W. 5; Gibbs, Richard A. 6; Highlander, Sarah K. 6,15; Weinstock, George M. 7; Wilson, Richard K. 7; White, Owen 3
[Article]
Nature.
486(7402):215-221, June 14, 2012.
(Format: HTML, PDF)
: 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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