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Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower,Dirk Gevers,Rob Knight,Sahar Abubucker,Jonathan H. Badger,Asif T. Chinwalla,Heather Huot Creasy,Ashlee M. Earl,Michael Fitzgerald,Robert S. Fulton,Michelle Giglio,Kymberlie Hallsworth-Pepin,Elizabeth A. Lobos,Ramana Madupu,Vincent Magrini,John Martin,Makedonka Mitreva,Donna M. Muzny,Erica Sodergren,James Versalovic,Aye Wollam,Kim C. Worley,Jennifer Wortman,Sarah Young,Qiandong Zeng,Kjersti M. Aagaard,Olukemi O. Abolude,Emma Allen‐Vercoe,Eric J. Alm,Lucía Alvarado,Gary L. Andersen,Scott Anderson,Elizabeth L. Appelbaum,Harindra Arachchi,Gary C. Armitage,Cesar Arze,Tulin Ayvaz,Carl C. Baker,Lisa Begg,Tsegahiwot Belachew,Veena Bhonagiri,Monika Bihan,Martin J. Blaser,Toby Bloom,Vivien Bonazzi,J. Paul Brooks,Gregory A. Buck,Christian Buhay,Dana Busam,J Campbell,Shane Canon,Brandi L. Cantarel,Patrick Chain,I. Min A. Chen,Lei Chen,Shaila Chhibba,Ken Chu,Dawn Ciulla,José C. Clemente,Sandra W. Clifton,Sean Conlan,Jonathan Crabtree,Mary A. Cutting,Noam J. Davidovics,Catherine Davis,Todd Z. DeSantis,Carolyn Deal,Kimberley D. Delehaunty,Floyd E. Dewhirst,Elena Deych,Yan Ding,David J. Dooling,Shannon Dugan,W. Michael Dunne,A. Scott Durkin,Robert C. Edgar,Rachel Erlich,Candace N. Farmer,Ruth M. Farrell,Karoline Faust,Michael Feldgarden,Victor Felix,Sheila Fisher,Anthony A. Fodor,Larry J. Forney,Leslie Foster,Valentina Di Francesco,Jonathan Friedman,Dennis Friedrich,Catrina C. Fronick,Lucinda L. Fulton,Hongyu Gao,Nathalia Garcia,Georgia Giannoukos,Christina Giblin,Maria Y. Giovanni,Jonathan M. Goldberg,Johannes Goll,Antonio G. González,Allison Griggs,Sharvari Gujja,Susan Kinder Haake,Brian J. Haas,Holli Hamilton,Emily Harris,Theresa A. Hepburn,Brandi Herter,Diane E. Hoffmann,Michael Holder,Clinton Howarth,Katherine Huang,Susan M. Huse,Jacques Izard,Janet Jansson,Huaiyang Jiang,Catherine Jordan,Vandita Joshi,James A. Katancik,Wendy A. Keitel,Scott T. Kelley,Cristyn Kells,Nicholas B. King,Dan Knights,Heidi H. Kong,Omry Koren,Sergey Koren,Karthik Kota,Christie Kovar,Nikos C. Kyrpides,Patricio S. La Rosa,Sandra L. Lee,Katherine P. Lemon,Niall J. Lennon,Cecil M. Lewis,Lora Lewis,Ruth E. Ley,Kelvin Li,Konstantinos Liolios,Bo Liu,Yue Liu,Chien-Chi Lo,Catherine Lozupone,R. Dwayne Lunsford,Tessa Madden,Anup Mahurkar,Peter Mannon,Elaine R. Mardis,Victor Markowitz,Konstantinos Mavromatis,Jamison McCorrison,Daniel McDonald,Jean McEwen,Amy L. McGuire,Pamela McInnes,Teena Mehta,Kathie A. Mihindukulasuriya,Jason R. Miller,Patrick Minx,Irene Newsham,Chad Nusbaum,Michelle Oglaughlin,Joshua Orvis,Ioanna Pagani,Krishna Palaniappan,Shital M. Patel,Matthew Pearson,Jane Peterson,Mircea Podar,Craig Pohl,Katherine S. Pollard,Mihai Pop,Margaret Priest,Lita M. Proctor,Xiang Qin,Jeroen Raes,Jacques Ravel,Jeffrey G. Reid,Mina Rho,Rosamond Rhodes,Kevin Riehle,Maria C. Rivera,Beltran Rodriguez-Mueller,Yu Hui Rogers,Matthew C. Ross,Carsten Russ,Ravi Sanka,Pamela Sankar,J. Fah Sathirapongsasuti,Jeffery A. Schloss,Patrick Schloß,Thomas M. Schmidt,Matthew Scholz,Lynn M. 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,Christopher Smillie,Jack D. Sobel,Daniel Sommer,Paul Spicer,Granger Sutton,Sean M. Sykes,Diana Tabbaa,Mathangi Thiagarajan,Chad Tomlinson,Manolito Torralba,Todd J. Treangen,Rebecca Truty,Tatiana A. Vishnivetskaya,Jason Walker,Lu Wang,Zhengyuan Wang,Doyle V. Ward,Wesley C. Warren,Mark A. Watson,Christopher Wellington,Kris A. Wetterstrand,James R. White,Katarzyna Wilczek-Boney,Yuanqing Wu,Kristine M. Wylie,Todd Wylie,Chandri Yandava,Ye Liang,Yuzhen Ye,Shibu Yooseph,Bonnie P. Youmans,Lan Zhang,Yanjiao Zhou,Yiping Zhu,Laurie Zoloth,Jeremy Zucker,Bruce W. Birren,Richard A. Gibbs,Sarah K. Highlander,Barbara Methé,Karen E. Nelson,Joseph F. Petrosino,George M. Weinstock,Richard K. Wilson,Owen White

Microbiome

Metagenomics

Biology

2012

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome. The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome. 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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“Structure, function and diversity of the healthy human microbiome” is a paper by Curtis Huttenhower Dirk Gevers Rob Knight Sahar Abubucker Jonathan H. Badger Asif T. Chinwalla Heather Huot Creasy Ashlee M. Earl Michael Fitzgerald Robert S. Fulton Michelle Giglio Kymberlie Hallsworth-Pepin Elizabeth A. Lobos Ramana Madupu Vincent Magrini John Martin Makedonka Mitreva Donna M. Muzny Erica Sodergren James Versalovic Aye Wollam Kim C. Worley Jennifer Wortman Sarah Young Qiandong Zeng Kjersti M. Aagaard Olukemi O. Abolude Emma Allen‐Vercoe Eric J. Alm Lucía Alvarado Gary L. Andersen Scott Anderson Elizabeth L. Appelbaum Harindra Arachchi Gary C. Armitage Cesar Arze Tulin Ayvaz Carl C. Baker Lisa Begg Tsegahiwot Belachew Veena Bhonagiri Monika Bihan Martin J. Blaser Toby Bloom Vivien Bonazzi J. Paul Brooks Gregory A. Buck Christian Buhay Dana Busam J Campbell Shane Canon Brandi L. Cantarel Patrick Chain I. Min A. Chen Lei Chen Shaila Chhibba Ken Chu Dawn Ciulla José C. Clemente Sandra W. Clifton Sean Conlan Jonathan Crabtree Mary A. Cutting Noam J. Davidovics Catherine Davis Todd Z. DeSantis Carolyn Deal Kimberley D. Delehaunty Floyd E. Dewhirst Elena Deych Yan Ding David J. Dooling Shannon Dugan W. Michael Dunne A. Scott Durkin Robert C. Edgar Rachel Erlich Candace N. Farmer Ruth M. Farrell Karoline Faust Michael Feldgarden Victor Felix Sheila Fisher Anthony A. Fodor Larry J. Forney Leslie Foster Valentina Di Francesco Jonathan Friedman Dennis Friedrich Catrina C. Fronick Lucinda L. Fulton Hongyu Gao Nathalia Garcia Georgia Giannoukos Christina Giblin Maria Y. Giovanni Jonathan M. Goldberg Johannes Goll Antonio G. González Allison Griggs Sharvari Gujja Susan Kinder Haake Brian J. Haas Holli Hamilton Emily Harris Theresa A. Hepburn Brandi Herter Diane E. Hoffmann Michael Holder Clinton Howarth Katherine Huang Susan M. Huse Jacques Izard Janet Jansson Huaiyang Jiang Catherine Jordan Vandita Joshi James A. Katancik Wendy A. Keitel Scott T. Kelley Cristyn Kells Nicholas B. King Dan Knights Heidi H. Kong Omry Koren Sergey Koren Karthik Kota Christie Kovar Nikos C. Kyrpides Patricio S. La Rosa Sandra L. Lee Katherine P. Lemon Niall J. Lennon Cecil M. Lewis Lora Lewis Ruth E. Ley Kelvin Li Konstantinos Liolios Bo Liu Yue Liu Chien-Chi Lo Catherine Lozupone R. Dwayne Lunsford Tessa Madden Anup Mahurkar Peter Mannon Elaine R. Mardis Victor Markowitz Konstantinos Mavromatis Jamison McCorrison Daniel McDonald Jean McEwen Amy L. McGuire Pamela McInnes Teena Mehta Kathie A. Mihindukulasuriya Jason R. Miller Patrick Minx Irene Newsham Chad Nusbaum Michelle Oglaughlin Joshua Orvis Ioanna Pagani Krishna Palaniappan Shital M. Patel Matthew Pearson Jane Peterson Mircea Podar Craig Pohl Katherine S. Pollard Mihai Pop Margaret Priest Lita M. Proctor Xiang Qin Jeroen Raes Jacques Ravel Jeffrey G. Reid Mina Rho Rosamond Rhodes Kevin Riehle Maria C. Rivera Beltran Rodriguez-Mueller Yu Hui Rogers Matthew C. Ross Carsten Russ Ravi Sanka Pamela Sankar J. Fah Sathirapongsasuti Jeffery A. Schloss Patrick Schloß Thomas M. Schmidt Matthew Scholz Lynn M. 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 Christopher Smillie Jack D. Sobel Daniel Sommer Paul Spicer Granger Sutton Sean M. Sykes Diana Tabbaa Mathangi Thiagarajan Chad Tomlinson Manolito Torralba Todd J. Treangen Rebecca Truty Tatiana A. Vishnivetskaya Jason Walker Lu Wang Zhengyuan Wang Doyle V. Ward Wesley C. Warren Mark A. Watson Christopher Wellington Kris A. Wetterstrand James R. White Katarzyna Wilczek-Boney Yuanqing Wu Kristine M. Wylie Todd Wylie Chandri Yandava Ye Liang Yuzhen Ye Shibu Yooseph Bonnie P. Youmans Lan Zhang Yanjiao Zhou Yiping Zhu Laurie Zoloth Jeremy Zucker Bruce W. Birren Richard A. Gibbs Sarah K. Highlander Barbara Methé Karen E. Nelson Joseph F. Petrosino George M. Weinstock Richard K. Wilson Owen White published in 2012. It has an Open Access status of “hybrid”. You can read and download a PDF Full Text of this paper here.