A framework for human microbiome research
Ravi Sanka(J. Craig Venter Institute), Johannes B. Goll(J. Craig Venter Institute), Jason Miller(J. Craig Venter Institute), Leslie Foster(University of Maryland, Baltimore), Karen E. Nelson(University of Maryland, Baltimore), A. Scott Durkin(Broad Institute), Jamison McCorrison(Broad Institute), Manolito Torralba(J. Craig Venter Institute), Indresh Singh(J. Craig Venter Institute), Yu-Hui Rogers(J. Craig Venter Institute), Ramana Madupu(J. Craig Venter Institute), Dana Busam(Broad Institute), Barbara A. Methé(Broad Institute), Kelvin Li(J. Craig Venter Institute), Monika Bihan(J. Craig Venter Institute), Granger G. Sutton(J. Craig Venter Institute), Mathangi Thiagarajan(J. Craig Venter Institute), Bo Liu(Washington University in St. Louis), Daniel D. Sommer(Washington University in St. Louis), Mihai Pop(Washington University in St. Louis), Sergey Koren(Baylor College of Medicine), Jonathan Crabtree(University of Maryland, Baltimore), Cesar Arze(University of Maryland, Baltimore), Lynn M. Schriml(University of Maryland, Baltimore), Anup Mahurkar(University of Maryland, Baltimore), Brandi L. Cantarel(Broad Institute), Owen White(Broad Institute), Victor Felix(Broad Institute), James R. White(University of Maryland, Baltimore), Jacques Ravel(University of Maryland, Baltimore), Olukemi O. Abolude(University of Maryland, Baltimore), Michelle Giglio(Broad Institute), Heather H. Creasy(Broad Institute), Catherine Jordan(University of Maryland, Baltimore), Joshua Orvis(Broad Institute), Noam J. Davidovics(University of Maryland, Baltimore), J. Fah Sathirapongsasuti(Broad Institute), Curtis Huttenhower(Broad Institute), Nicola Segata(University of Maryland, Baltimore), Theresa A. Hepburn(Broad Institute), Georgia Giannoukos(Broad Institute), Chad Nusbaum(Broad Institute), Diana Tabbaa(Broad Institute), Sharvari Gujja(Broad Institute), Jonathan M. Goldberg(Broad Institute), Eric J. Alm(Broad Institute), Ashlee M. Earl(Broad Institute), Brian J. Haas(Broad Institute), Sarah Young(Broad Institute), Michael Feldgarden(Broad Institute), Narmada Shenoy(Broad Institute), Dirk Gevers(Broad Institute), Jennifer R. Wortman(Broad Institute), M.A. Pearson(Broad Institute), Zhengyuan Wang(Broad Institute), Chandri Yandava(Broad Institute), Margaret Priest(Broad Institute), Jeremy Zucker(Broad Institute), Curtis Huttenhower(Broad Institute), Scott Anderson(Broad Institute), Sheila Fisher(Broad Institute), Katherine Huang(Broad Institute), Doyle V. Ward(Broad Institute), Dennis C. Friedrich(Broad Institute), Clinton Howarth(Broad Institute), Cristyn Kells(Broad Institute), Bruce W. Birren(Broad Institute), Qiandong Zeng(Broad Institute), Carsten Russ(Broad Institute), Toby Bloom(Broad Institute), Lucia Alvarado(Broad Institute), Allison Griggs(Broad Institute), Michael G. FitzGerald(Broad Institute), Dawn Ciulla(Broad Institute), Teena Mehta(Broad Institute), Harindra Arachchi(Broad Institute), Rachel Erlich(Broad Institute), Sean M. Sykes(Broad Institute), Yiming Zhu(Baylor College of Medicine), Richard A. Gibbs(Broad Institute), Vandita Joshi(Baylor College of Medicine), Sarah K. Highlander(Cleveland Clinic), Lan Zhang(Vrije Universiteit Brussel), Huaiyang Jiang(Broad Institute), Yue Liu(University of Maryland, Baltimore), Katarzyna Wilczek-Boney(Broad Institute), Irene Newsham(University of North Carolina at Charlotte), Kim C. Worley(University of Idaho), Lora Lewis(J. Craig Venter Institute), Michael Holder(National Institutes of Health), Niall J. Lennon(Baylor College of Medicine), Shannon Dugan(Broad Institute), Jeffrey G. Reid(Baylor College of Medicine), Yan Ding(Baylor College of Medicine), Donna M. Muzny(Baylor College of Medicine), Joseph F. Petrosino(Baylor College of Medicine), Xiang Qin(Broad Institute), Christian Buhay(National Institutes of Health), Sandra L. Lee(National Institutes of Health), Christie Kovar(Broad Institute), Yuan Qing Wu(J. Craig Venter Institute), Asif Chinwalla(University of Colorado Boulder), Patrick Minx(Broad Institute), Jason Walker(Broad Institute), David J. Dooling(Broad Institute), Sandra W. Clifton(National Institutes of Health), Wesley C. Warren(National Institutes of Health), Lucinda Fulton(Broad Institute), Kristine M. Wylie(Washington University in St. Louis), Chad Tomlinson(University of Maryland, Baltimore), Brandi Herter(Baylor College of Medicine), Todd Wylie(Broad Institute), Elaine R. Mardis(Broad Institute), Vincent Magrini(Marine Biological Laboratory), Kathie A. Mihindukulasuriya(Washington University in St. Louis), Richard K. Wilson(Lawrence Berkeley National Laboratory), Kimberley D. Delehaunty(Baylor College of Medicine), Sahar Abubucker(University of Maryland, Baltimore), George M. Weinstock(Baylor College of Medicine), John C. Martin(Washington University in St. Louis), Liang Ye(Baylor College of Medicine), Karthik Kota(Washington University in St. Louis), Veena Bhonagiri(Broad Institute), Elizabeth L. Appelbaum(University of California, Los Angeles), Yanjiao Zhou(Washington University in St. Louis), Michelle O’Laughlin(Howard Hughes Medical Institute), Kymberlie Hallsworth-Pepin(University of Colorado Boulder), Elizabeth A. Lobos(National Institutes of Health), Aye Wollam(Washington University in St. Louis), Catrina C. Fronick(Washington University in St. Louis), Makedonka Mitreva(Washington University in St. Louis), Elena Deych(Baylor College of Medicine), Craig Pohl(United States Department of Energy), Candace N. Farmer(Washington University in St. Louis), Robert S. Fulton(Baylor College of Medicine), Erica Sodergren(Washington University in St. Louis), Lei Chen(Baylor College of Medicine), James Versalovic(Baylor College of Medicine), Hongyu Gao(Baylor College of Medicine), James Versalovic(Baylor College of Medicine), Kjersti M. Aagaard(J. Craig Venter Institute), Emma Allen‐Vercoe(United States Department of Energy), Eric J. Alm(Broad Institute), Gary L. Andersen(Lawrence Berkeley National Laboratory), Gary C. Armitage(Los Alamos National Laboratory), Matthew C. Ross(Baylor College of Medicine), Sarah K. Highlander(National Institutes of Health), Joseph F. Petrosino(Baylor College of Medicine), Bonnie P. Youmans(University of Maryland, Baltimore), Tulin Ayvaz(Baylor College of Medicine), Wendy A. Keitel(Baylor College of Medicine), Carl C. Baker(United States Department of Energy), Lisa Begg(United States Department of Energy), Christina Giblin(J. Craig Venter Institute), Joseph L. Campbell(University of Colorado Boulder), Tsegahiwot Belachew(National Institutes of Health), Maria Y. Giovanni(Baylor College of Medicine), Carolyn Deal(National Institutes of Health), Valentina Di Francesco(Broad Institute), Martin J. Blaser(Washington University in St. Louis), Lu Wang(J. Craig Venter Institute), Kris A. Wetterstrand(Washington University in St. Louis), Jane L. Peterson(Baylor College of Medicine), Joseph L. Campbell(Broad Institute), Lita M. Proctor(Washington University in St. Louis), Vivien Bonazzi(University of Maryland, Baltimore), Christopher Wellington (United States Department of Energy), Shaila Chhibba(Lawrence Berkeley National Laboratory), Jean E. McEwen(Baylor College of Medicine), Jeffery A. Schloss(Broad Institute), Paul Brooks(National Institutes of Health), Gregory A. Buck(Oak Ridge National Laboratory), Nihar U. Sheth(Virginia Commonwealth University), Maria C. Rivera(University of California, San Francisco), Paul Brooks(Broad Institute), Maria C. Rivera(National Institutes of Health), Gregory A. Buck (Baylor College of Medicine), Shane R. Canon(Vrije Universiteit Brussel), Matthew Scholz(University of Maryland, Baltimore), Chien-Chi Lo (Los Alamos National Laboratory), Patrick Chain(Los Alamos National Laboratory), Victor Markowitz(Lawrence Berkeley National Laboratory), Ioanna Pagani(Baylor College of Medicine), Konstantinos Mavrommatis(Virginia Commonwealth University), Patrick Chain(Los Alamos National Laboratory), Konstantinos Liolios(J. Craig Venter Institute), Nikos C. Kyrpides(Baylor College of Medicine), Victor Markowitz(Broad Institute), Krishna Palaniappan(J. Craig Venter Institute), I-Min A. Chen(Lawrence Berkeley National Laboratory), Ken Chu(Lawrence Berkeley National Laboratory), Catherine Lozupone(National Institutes of Health), José C. Clemente(University of Colorado Boulder), Rob Knight(Howard Hughes Medical Institute), Daniel McDonald(Los Alamos National Laboratory), R. Dwayne Lunsford(University of Maryland, Baltimore), Mary A. Cutting(University of Michigan), Emily Harris(Harvard University Press), Pamela McInnes(National Institutes of Health), Holli Hamilton(Washington University in St. Louis), Catherine Davis(Cleveland Clinic), Todd Z. DeSantis(University of California, San Francisco), Katherine P. Lemon(Broad Institute), Floyd E. Dewhirst(Harvard University), Jacques Izard(Harvard University), Floyd E. Dewhirst(J. Craig Venter Institute), W. Michael Dunne(Washington University in St. Louis), Mark A. Watson(Wayne State University), W. Michael Dunne(Washington University in St. Louis), R. C. Edgar(Tiburon Associates (United States)), Richard R. Sharp(J. Craig Venter Institute), Ruth M. Farrell(Broad Institute), Jeroen Raes(Broad Institute), Karoline Faust(J. Craig Venter Institute), Jeroen Raes(Vrije Universiteit Brussel), Karoline Faust(J. Craig Venter Institute), Anthony A. Fodor(University of North Carolina at Charlotte), Larry J. Forney(University of Idaho), Jonathan Friedman(Oak Ridge National Laboratory), Christopher S. Smillie(Washington University in St. Louis), Nathalia Garcia(National Institutes of Health), Antonio González(Broad Institute), Dan Knights(Broad Institute), Diane E. Hoffmann(University of Maryland, Baltimore), Susan M. Huse(Marine Biological Laboratory), Jacques Izard(National Institutes of Health), Janet Jansson(National Institutes of Health), James A. Katancik(University of Maryland, Baltimore), Scott T. Kelley(Baylor College of Medicine), Beltran Rodriguez-Mueller(Baylor College of Medicine), Susan Kinder-Haake(Washington University in St. Louis), Nicholas B. King(Washington University in St. Louis), Rob Knight(Broad Institute), Heidi H. Kong(National Institutes of Health), Ruth E. Ley(Cornell University), Omry Koren(J. Craig Venter Institute), William D. Shannon(Baylor College of Medicine), Patricio S. La Rosa(Baylor College of Medicine), Katherine P. Lemon(Boston Children's Hospital), Paul Spicer(Baylor College of Medicine), Cecil M. Lewis(Northwestern University), Tessa Madden(Broad Institute), Peter Mannon(Broad Institute), Amy L. McGuire(Baylor College of Medicine), Shital M. Patel(Baylor College of Medicine), Mircea Podar(Oak Ridge National Laboratory), Tatiana A. Vishnivetskaya(Oak Ridge National Laboratory), Thomas J. Sharpton(University of Maryland, Baltimore), Katherine S. Pollard(Gladstone Institutes), Rebecca Truty(Gladstone Institutes), Katherine S. Pollard(Gladstone Institutes), Katherine S. Pollard(Gladstone Institutes), Jacques Ravel(University of Maryland, Baltimore), Mina Rho(Indiana University Bloomington), Yuzhen Ye(Indiana University Bloomington), Rosamond Rhodes(Icahn School of Medicine at Mount Sinai), Kevin Riehle(Baylor College of Medicine), Pamela Sankar(Center for Practical Bioethics), Patrick D. Schloss(University of Michigan), Alyxandria M. Schubert(University of Michigan), Thomas M. Schmidt(Michigan State University), Gina Simone(Emmes (United States)), Jack D. Sobel(Harper University Hospital), Todd J. Treangen(Johns Hopkins University), Jonathan H. Badger(J. Craig Venter Institute), Shibu Yooseph(J. Craig Venter Institute), Laurie Zoloth(Northwestern University), Joseph F. Petrosino(Baylor College of Medicine), Julia A. Segre(National Human Genome Research Institute), Sean Conlan(National Human Genome Research Institute)
Cited by 2,744Open Access
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. 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 inhabit and interact with the human body in sickness and in health. In two Articles in this issue of Nature, the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years.
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