A framework for human microbiome research

Barbara A. Methé, Karen E. Nelson, Mihai Pop, Heather H. Creasy, Michelle G. Giglio, Curtis Huttenhower, Dirk Gevers, Joseph F. Petrosino, Sahar Abubucker, Jonathan H. Badger, Asif T. Chinwalla, Ashlee M. Earl, Michael G. Fitzgerald, Robert S. Fulton, Kymberlie Hallsworth-Pepin, Elizabeth A. Lobos, Ramana Madupu, Vincent Magrini, John C. Martin, Makedonka MitrevaDonna 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 R. Bonazzi, Paul Brooks, Gregory A. Buck, Christian J. Buhay, Dana A. Busam, Joseph L. Campbell, Shane R. Canon, Brandi L. Cantarel, Patrick S. 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, W. 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 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, 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, Susan Kinder-Haake, Nicholas B. King, Rob Knight, 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 Mavrommatis, 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 O'Laughlin, Joshua Orvis, Ioanna Pagani, Krishna Palaniappan, Shital M. Patel, Matthew Pearson, Jane Peterson, Mircea Podar, Craig Pohl, Katherine S. Pollard, 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, Chris 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, Yuan Qing 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, George M. Weinstock, Richard K. Wilson, Owen White

Research output: Contribution to journalArticle

1294 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)215-221
Number of pages7
JournalNature
Volume486
Issue number7402
DOIs
StatePublished - Jun 14 2012

ASJC Scopus subject areas

  • General

Fingerprint Dive into the research topics of 'A framework for human microbiome research'. Together they form a unique fingerprint.

  • Cite this

    Methé, B. A., Nelson, K. E., Pop, M., Creasy, H. H., Giglio, M. G., Huttenhower, C., Gevers, D., Petrosino, J. F., Abubucker, S., Badger, J. H., Chinwalla, A. T., Earl, A. M., Fitzgerald, M. G., Fulton, R. S., Hallsworth-Pepin, K., Lobos, E. A., Madupu, R., Magrini, V., Martin, J. C., ... White, O. (2012). A framework for human microbiome research. Nature, 486(7402), 215-221. https://doi.org/10.1038/nature11209