Human gut microbiome viewed across age and geography
Tanya Yatsunenko,Federico E. Rey,Mark J. Manary,Mark J. Manary,Indi Trehan,Indi Trehan,Maria Gloria Dominguez-Bello,Monica Contreras,Magda Magris,Glida Hidalgo,Robert N. Baldassano,Andrey P. Anokhin,Andrew C. Heath,Barbara B. Warner,Jens Reeder,Justin Kuczynski,J. Gregory Caporaso,Catherine A. Lozupone,Christian L. Lauber,Jose C. Clemente,Dan Knights,Rob Knight,Jeffrey I. Gordon +22 more
Reads0
Chats0
TLDR
The need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization is underscored, as distinctive features of the functional maturation of the gut microbiome are evident in early infancy as well as adulthood.Abstract:
Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.read more
Citations
More filters
Journal ArticleDOI
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
Daryl M. Gohl,Pajau Vangay,John R. Garbe,Allison MacLean,Adam Hauge,Aaron Becker,Trevor J. Gould,Jonathan B. Clayton,Timothy J. Johnson,Ryan C. Hunter,Dan Knights,Kenneth B. Beckman +11 more
TL;DR: This work analyzes the amplification process to reveal insights into sources of experimental error and bias in amplicon-based microbial community and microbiome experiments and presents a method that improves on the current best practices and enables the detection of taxonomic groups that often go undetected with existing methods.
Journal ArticleDOI
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study
Tommi Vatanen,Eric A. Franzosa,Eric A. Franzosa,Randall Schwager,Surya Tripathi,Timothy D. Arthur,Kendra Vehik,Åke Lernmark,William Hagopian,Marian Rewers,Jin-Xiong She,Jorma Toppari,Jorma Toppari,Anette-G. Ziegler,Beena Akolkar,Jeffrey P. Krischer,Christopher J. Stewart,Christopher J. Stewart,Nadim J. Ajami,Joseph F. Petrosino,Dirk Gevers,Dirk Gevers,Harri Lähdesmäki,Hera Vlamakis,Curtis Huttenhower,Curtis Huttenhower,Ramnik J. Xavier,Ramnik J. Xavier,Ramnik J. Xavier +28 more
TL;DR: An analysis of more than 10,000 metagenomes from the TEDDY study provides a detailed functional profile of the gut microbiome in relation to islet autoimmunity, and supports the protective effects of short-chain fatty acids in early-onset type 1 diabetes.
Journal ArticleDOI
Towards standards for human fecal sample processing in metagenomic studies
Paul I. Costea,Georg Zeller,Shinichi Sunagawa,Eric Pelletier,Eric Pelletier,Adriana Alberti,Florence Levenez,Melanie Tramontano,Marja Driessen,Rajna Hercog,Ferris Elias Jung,Jens Roat Kultima,Matthew R. Hayward,Luis Pedro Coelho,Emma Allen-Vercoe,Laurie Bertrand,Michael Blaut,Jillian R.M. Brown,Thomas Carton,Stéphanie Cools-Portier,Michelle C. Daigneault,Muriel Derrien,Anne Druesne,Willem M. de Vos,Willem M. de Vos,B. Brett Finlay,Harry J. Flint,Francisco Guarner,Masahira Hattori,Masahira Hattori,Hans G.H.J. Heilig,Ruth Ann Luna,Johan E. T. van Hylckama Vlieg,Jana Junick,Ingeborg Klymiuk,Philippe Langella,Volker Mai,Chaysavanh Manichanh,Jennifer C. Martin,Clémentine Mery,Hidetoshi Morita,Paul W. O'Toole,Céline Orvain,Kiran Raosaheb Patil,John Penders,Søren Persson,Nicolas Pons,Milena Popova,Anne Salonen,Delphine M. Saulnier,Karen P. Scott,Bhagirath Singh,Kathleen Slezak,Patrick Veiga,James Versalovic,Liping Zhao,Erwin G. Zoetendal,S. Dusko Ehrlich,S. Dusko Ehrlich,Joël Doré,Peer Bork +60 more
TL;DR: A standardized DNA extraction method for human fecal samples is recommended, for which transferability across labs was established and which was further benchmarked using a mock community of known composition to improve comparability of human gut microbiome studies and facilitate meta-analyses.
Journal ArticleDOI
Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development.
Adam R. Burns,W. Zac Stephens,Keaton Stagaman,Sandi Wong,Sandi Wong,John F. Rawls,Karen Guillemin,Brendan J. M. Bohannan +7 more
TL;DR: It is demonstrated that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggested that potentially unique or important taxa may be identified by their divergence from neutral distributions.
Journal ArticleDOI
The Human Gut Microbiome: From Association to Modulation
TL;DR: The type of studies that will be essential for translating microbiome research into targeted modulations with dedicated benefits for the human host are discussed.
References
More filters
Journal ArticleDOI
QIIME allows analysis of high-throughput community sequencing data.
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.
Classification and Regression by randomForest
Andy Liaw,Matthew C. Wiener +1 more
TL;DR: random forests are proposed, which add an additional layer of randomness to bagging and are robust against overfitting, and the randomForest package provides an R interface to the Fortran programs by Breiman and Cutler.
Journal ArticleDOI
Silhouettes: a graphical aid to the interpretation and validation of cluster analysis
TL;DR: A new graphical display is proposed for partitioning techniques, where each cluster is represented by a so-called silhouette, which is based on the comparison of its tightness and separation, and provides an evaluation of clustering validity.
Book
Finding Groups in Data: An Introduction to Cluster Analysis
TL;DR: An electrical signal transmission system, applicable to the transmission of signals from trackside hot box detector equipment for railroad locomotives and rolling stock, wherein a basic pulse train is transmitted whereof the pulses are of a selected first amplitude and represent a train axle count.
Journal ArticleDOI
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
TL;DR: The Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals are described, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species.
Related Papers (5)
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
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
QIIME allows analysis of high-throughput community sequencing data.
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