A framework for human microbiome research

Human Microbiome Project Consortium, 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 Mitreva, Donna 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 Jr, 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, Human Microbiome Project Consortium, 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 Mitreva, Donna 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 Jr, 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

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.

Conflict of interest statement

Competing Interests Statement

The authors declare that they have no competing interests.

Figures

Figure 1. Rates of gene and OTU…
Figure 1. Rates of gene and OTU discovery from HMP taxonomic and metagenomic data
Accumulation curves for a, OTU counts from 16S data (all body sites) b, clustered gene index counts from metagenomic data (all applicable body sites) and c, the ratio of average unique genes contributed versus unique OTUs encountered with increasing sample counts (Supplementary Information). Ratios given for each curve in c represent the average number of unique genes contributed per unique OTU at the final sample count. Curves for stool, buccal mucosa and anterior nares suggest that the proportion of gene-to-taxa discovery has stabilized. In contrast, the curve for supragingival plaque suggests relatively fewer new genes are being contributed per additional OTU. Error bars represent 95% confidence intervals.

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Source: PubMed

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