Structure, function and diversity of the healthy human microbiome
Curtis Huttenhower,Curtis Huttenhower,Dirk Gevers,Rob Knight,Rob Knight,Sahar Abubucker,Jonathan H. Badger,Asif T. Chinwalla,Heather Huot Creasy,Ashlee M. Earl,Michael Fitzgerald,Robert S. Fulton,Michelle G. 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 R. Wortman,Sarah Young,Qiandong Zeng,Kjersti Aagaard,Olukemi O. Abolude,Emma Allen-Vercoe,Eric J. Alm,Eric J. Alm,Lucia 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 J. Buhay,Dana A. Busam,Joseph L. Campbell,Shane Canon,Brandi L. Cantarel,Patrick S. G. Chain,Patrick S. G. Chain,I. Min A. Chen,Lei Chen,Shaila Chhibba,Ken Chu,Dawn 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 Dugan,Wm. Michael Dunne,Wm. Michael Dunne,A. Scott Durkin,Robert C. Edgar,Rachel L. 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 C. Friedrich,Catrina Fronick,Lucinda Fulton,Hongyu Gao,Nathalia Garcia,Georgia Giannoukos,Christina Giblin,Maria Y. Giovanni,Jonathan M. Goldberg,Johannes B. Goll,Antonio Gonzalez,Allison D. Griggs,Sharvari Gujja,Susan Kinder Haake,Brian J. Haas,Holli A. Hamilton,Emily L. Harris,Theresa A. Hepburn,Brandi Herter,Diane E. Hoffmann,Michael 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,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 A. Lozupone,R. Dwayne Lunsford,Tessa Madden,Anup Mahurkar,Peter J. Mannon,Elaine R. Mardis,Victor M. Markowitz,Victor M. Markowitz,Konstantinos Mavromatis,Jamison McCorrison,Daniel McDonald,Jean E. 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 D. 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 D. Schloss,Thomas M. Schmidt,Matthew B. 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 D. Sommer,Paul Spicer,Granger G. 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,Liang Ye,Yuzhen Ye,Shibu Yooseph,Bonnie P. Youmans,Lan Zhang,Yanjiao Zhou,Yiming Zhu,Laurie Zoloth,Jeremy Zucker,Bruce W. Birren,Richard A. Gibbs,Sarah K. Highlander,Barbara A. Methé,Karen E. Nelson,Joseph F. Petrosino,George M. Weinstock,Richard K. Wilson,Owen White +253 more
TLDR
The Human Microbiome Project Consortium reported 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 as discussed by the authors.Abstract:
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.read more
Citations
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Population-level analysis of gut microbiome variation
Gwen Falony,Marie Joossens,Marie Joossens,Sara Vieira-Silva,Jun Wang,Youssef Darzi,Youssef Darzi,Karoline Faust,Karoline Faust,Alexander Kurilshikov,Marc Jan Bonder,Mireia Valles-Colomer,Doris Vandeputte,Doris Vandeputte,Raul Y. Tito,Raul Y. Tito,Samuel Chaffron,Samuel Chaffron,Leen Rymenans,Leen Rymenans,Chloë Verspecht,Lise De Sutter,Lise De Sutter,Gipsi Lima-Mendez,Kevin D'hoe,Kevin D'hoe,Karl Jonckheere,Karl Jonckheere,Daniel Homola,Daniel Homola,Roberto Garcia,Roberto Garcia,Ettje F. Tigchelaar,Linda Eeckhaudt,Linda Eeckhaudt,Jingyuan Fu,Liesbet Henckaerts,Alexandra Zhernakova,Cisca Wijmenga,Jeroen Raes,Jeroen Raes +40 more
TL;DR: Stool consistency showed the largest effect size, whereas medication explained largest total variance and interacted with other covariate-microbiota associations, and proposed disease marker genera associated to host covariates were found associated to microbiota compositional variation with a 92% replication rate.
Journal ArticleDOI
Alterations of the human gut microbiome in liver cirrhosis
Nan Qin,Fengling Yang,Ang Li,Edi Prifti,Yanfei Chen,Li Shao,Jing Guo,Jian Yao,Lingjiao Wu,Jiawei Zhou,Ni Shujun,Lin Liu,Nicolas Pons,Jean-Michel Batto,Sean Kennedy,Pierre Leonard,Chunhui Yuan,Wenchao Ding,Yuanting Chen,Xinjun Hu,Beiwen Zheng,Guirong Qian,Wei Xu,S. Dusko Ehrlich,Shu-Sen Zheng,Lanjuan Li +25 more
TL;DR: The gut microbiome in liver cirrhosis is characterized by comparing 98 patients and 83 healthy control individuals and on the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort, suggesting microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.
Journal ArticleDOI
Tryptophan Catabolites from Microbiota Engage Aryl Hydrocarbon Receptor and Balance Mucosal Reactivity via Interleukin-22
Teresa Zelante,Rossana G. Iannitti,Cristina Cunha,Antonella De Luca,Gloria Giovannini,Giuseppe Pieraccini,Riccardo Zecchi,Carmen D'Angelo,Cristina Massi-Benedetti,Francesca Fallarino,Agostinho Carvalho,Paolo Puccetti,Luigina Romani +12 more
TL;DR: A metabolic pathway whereby Trp metabolites from the microbiota balance mucosal reactivity in mice is described, whereby highly adaptive lactobacilli are expanded and produce an aryl hydrocarbon receptor (AhR) ligand-indole-3-aldehyde-that contributes to AhR-dependent Il22 transcription.
Journal ArticleDOI
Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy
Omry Koren,Julia K. Goodrich,Tyler C. Cullender,Aymé Spor,Kirsi Laitinen,Helene Kling Bäckhed,Antonio Gonzalez,Jeffrey J. Werner,Largus T. Angenent,Rob Knight,Rob Knight,Fredrik Bäckhed,Erika Isolauri,Seppo Salminen,Ruth E. Ley +14 more
TL;DR: It is indicated that host-microbial interactions that impact host metabolism can occur and may be beneficial in pregnancy and when transferred to germ-free mice, T3 microbiota induced greater adiposity and insulin insensitivity compared to T1.
Journal ArticleDOI
Binning metagenomic contigs by coverage and composition
Johannes Alneberg,Brynjar Smari Bjarnason,Ino de Bruijn,Melanie Schirmer,Joshua Quick,Umer Zeeshan Ijaz,Leo Lahti,Nicholas J. Loman,Anders F. Andersson,Christopher Quince +9 more
TL;DR: ConCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes is presented, demonstrating high recall and precision on artificial as well as real human gut metagenome data sets.
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J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
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A human gut microbial gene catalogue established by metagenomic sequencing
Junjie Qin,Ruiqiang Li,Jeroen Raes,Manimozhiyan Arumugam,Kristoffer Sølvsten Burgdorf,Chaysavanh Manichanh,Trine Nielsen,Nicolas Pons,Florence Levenez,Takuji Yamada,Daniel R. Mende,Junhua Li,Junming Xu,Shaochuan Li,Dongfang Li,Jianjun Cao,Bo Wang,Huiqing Liang,Huisong Zheng,Yinlong Xie,Julien Tap,Patricia Lepage,Marcelo Bertalan,Jean-Michel Batto,Torben Hansen,Denis Le Paslier,Allan Linneberg,H. Bjørn Nielsen,Eric Pelletier,Pierre Renault,Thomas Sicheritz-Pontén,Keith Turner,Hongmei Zhu,Chang Yu,Shengting Li,Min Jian,Yan Zhou,Yingrui Li,Xiuqing Zhang,Songgang Li,Nan Qin,Huanming Yang,Jian Wang,Søren Brunak,Joël Doré,Francisco Guarner,Karsten Kristiansen,Oluf Pedersen,Julian Parkhill,Jean Weissenbach,Peer Bork,S. Dusko Ehrlich,Jun Wang +52 more
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Peter J. Turnbaugh,Micah Hamady,Tanya Yatsunenko,Brandi L. Cantarel,Alexis E. Duncan,Ruth E. Ley,Mitchell L. Sogin,William J. Jones,Bruce A. Roe,Jason P. Affourtit,Michael Egholm,Bernard Henrissat,Andrew C. Heath,Rob Knight,Jeffrey I. Gordon +14 more
TL;DR: The faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers are characterized to address how host genotype, environmental exposure and host adiposity influence the gut microbiome.
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Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
Harry Sokol,Bénédicte Pigneur,Laurie Watterlot,Omar Lakhdari,Luis G. Bermúdez-Humarán,Jean-Jacques Gratadoux,Sébastien Blugeon,Chantal Bridonneau,Jean-Pierre Furet,Gérard Corthier,Corinne Grangette,Nadia Vasquez,Philippe Pochart,Germain Trugnan,Ginette Thomas,Hervé M. Blottière,Joël Doré,Philippe Marteau,Philippe Seksik,Philippe Langella +19 more
TL;DR: The results suggest that counterbalancing dysbiosis using F. prausnitzii as a probiotic is a promising strategy in CD treatment and exhibits anti-inflammatory effects on cellular and TNBS colitis models, partly due to secreted metabolites able to block NF-κB activation and IL-8 production.
Journal ArticleDOI
Vaginal microbiome of reproductive-age women
Jacques Ravel,Pawel Gajer,Zaid Abdo,G. Maria Schneider,Sara S. K. Koenig,Stacey L. McCulle,Shara Karlebach,Reshma Gorle,Jennifer Russell,Carol O. Tacket,Rebecca M. Brotman,Catherine C. Davis,Kevin A. Ault,Ligia Peralta,Larry J. Forney +14 more
TL;DR: The inherent differences within and between women in different ethnic groups strongly argues for a more refined definition of the kinds of bacterial communities normally found in healthy women and the need to appreciate differences between individuals so they can be taken into account in risk assessment and disease diagnosis.
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