A framework for human microbiome research

作者：Barbara A. Methé, Karen Nelson, Ramana Madupu, Monika Bihan, Dana Busam, A. Scott Durkin, Leslie Foster, Johannes B. Goll, Kelvin Li, Jamison McCorrison, Jason Miller, Yu-Hui Rogers, Ravi Sanka, Indresh Singh, Granger G. Sutton, Mathangi Thiagarajan, Manolito Torralba, Mihai Pop, Sergey Koren, Bo Liu, Daniel Sommer, Heather H. Creasy, Michelle Giglio, Olukemi O. Abolude, Cesar Arze, Brandi L. Cantarel, Jonathan Crabtree, Noam J. Davidovics, Victor Felix, Catherine Jordan, Anup Mahurkar, Joshua Orvis, Jacques Ravel, Lynn M. Schriml, James R. White, Owen White, Curtis Huttenhower, J. Fah Sathirapongsasuti, Nicola Segata, Dirk Gevers, Ashlee M. Earl, Michael G. FitzGerald, Jennifer R. Wortman, Sarah Young, Qiandong Zeng, Eric J. Alm, Lucia Alvarado, Scott Anderson, Harindra Arachchi, Toby Bloom, Dawn Ciulla, Rachel Erlich, Michael Feldgarden, Sheila Fisher, Dennis C. Friedrich, Georgia Giannoukos, Jonathan M. Goldberg, Allison Griggs, Sharvari Gujja, Brian J. Haas, Theresa A. Hepburn, Clinton Howarth, Katherine Huang, Cristyn Kells, Teena Mehta, Chad Nusbaum, M.A. Pearson, Margaret Priest, Carsten Russ, Narmada Shenoy, Sean M. Sykes, Diana Tabbaa, Zhengyuan Wang, Doyle V. Ward, Chandri Yandava, Jeremy Zucker, Bruce W. Birren, Joseph F. Petrosino, Donna M. Muzny, Kim C. Worley, Christian Buhay, Yan Ding, Shannon Dugan, Michael Holder, Huaiyang Jiang, Vandita Joshi, Christie Kovar, Sandra L. Lee, Niall J. Lennon, Lora Lewis, Yue Liu, Irene Newsham, Xiang Qin, Jeffrey G. Reid, Katarzyna Wilczek-Boney, Yuan Wu, Lan Zhang, Yiming Zhu, Richard A. Gibbs, Sarah K. Highlander, Sahar Abubucker, Asif Chinwalla, Robert S. Fulton, Kymberlie Hallsworth-Pepin, Elizabeth A. Lobos, Vincent Magrini, John C. Martin, Makedonka Mitreva, Erica Sodergren, Aye Wollam, Elizabeth L. Appelbaum, Veena Bhonagiri, Lei Chen, Sandra W. Clifton, Kimberley D. Delehaunty, Elena Deych, David J. Dooling, Candace N. Farmer, Catrina C. Fronick, Lucinda Fulton, Brandi Herter, Karthik Kota, Elaine R. Mardis, Kathie A. Mihindukulasuriya, Patrick Minx, Michelle O'Laughlin, Craig Pohl, Chad Tomlinson, Jason Walker, Wesley C. Warren, Kristine M. Wylie, Todd Wylie, Liang Ye, Yanjiao Zhou, George M. Weinstock, Richard K. Wilson, James Versalovic, Hongyu Gao, Kjersti M. Aagaard, Emma Allen‐Vercoe, Gary L. Andersen, Gary C. Armitage, Tulin Ayvaz, Wendy A. Keitel, Matthew C. Ross, Bonnie P. Youmans, Carl C. Baker, Lisa Begg, Tsegahiwot Belachew, Joseph L. Campbell, Carolyn Deal, Valentina Di Francesco, Christina Giblin, Maria Y. Giovanni, Martin J. Blaser, Vivien Bonazzi, Shaila Chhibba, Jean E. McEwen, Jane L. Peterson, Lita M. Proctor, Jeffery A. Schloss, Lu Wang, Christopher Wellington, Kris A. Wetterstrand, Paul Brooks, Gregory A. Buck, Maria C. Rivera, Nihar U. Sheth, Shane R. Canon, Patrick Chain, Chien‐Chi Lo, Matthew Scholz, Nikos C. Kyrpides, Konstantinos Liolios, Victor M. Markowitz, Konstantinos Mavrommatis, I Pagani, I-Min A. Chen, Ken Chu, K G Palaniappan, José C. Clemente, Rob Knight, Catherine Lozupone, Daniel McDonald, Mary A. Cutting, Holli Hamilton, Emily Harris, R. Dwayne Lunsford, Pamela McInnes, Catherine C. Davis, Todd Z. DeSantis, Floyd E. Dewhirst, Jacques Izard, Katherine P. Lemon, W. Michael Dunne, Mark A. Watson, R. C. Edgar, Ruth M. Farrell, Richard R. Sharp, Karoline Faust, Jeroen Raes, Anthony A. Fodor, Larry J. Forney, Jonathan Friedman, Christopher S. Smillie, Nathalia García, Antonio González, Dan Knights, Diane E. Hoffmann, Susan M. Huse, Janet Jansson, James A. Katancik, Scott T. Kelley, Beltran Rodriguez-Mueller, Susan Kinder-Haake, Nicholas B. King, Heidi H. Kong, Omry Koren, Ruth E. Ley, Patricio S. La Rosa, William D. Shannon, Cecil M. Lewis, Paul Spicer, Tessa Madden, Peter Mannon, Amy L. McGuire, Shital M. Patel, Mircea Podar, Tatiana A. Vishnivetskaya, Katherine S. Pollard, Thomas J. Sharpton, Rebecca Truty, Mina Rho, Yuzhen Ye, Rosamond Rhodes, Kevin Riehle, P Akshay Sankar, Patrick D. Schloss, Alyxandria M. Schubert, Thomas M. Schmidt, Gina A. Simone, Jack D. Sobel, Todd J. Treangen, Jonathan H. Badger, Shibu Yooseph, LAURIE ZOLOTH, Sean Conlan, Julia A. Segre · 发表于：Nature · 年份：2012 · DOI：10.1038/nature11209 · 被引用次数：2786 · 研究领域：Gut microbiota and health、Diet and metabolism studies、Probiotics and Fermented Foods

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. The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources. The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that in...