DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan,Paul J. McMurdie,Michael J. Rosen,Andrew W. Han,Amy Jo A. Johnson,Susan Holmes +5 more
TLDR
The open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors is presented, revealing a diversity of previously undetected Lactobacillus crispatus variants.Abstract:
We present the open-source software package DADA2 for modeling and correcting Illumina-sequenced amplicon errors (https://github.com/benjjneb/dada2). DADA2 infers sample sequences exactly and resolves differences of as little as 1 nucleotide. In several mock communities, DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.read more
Citations
More filters
Journal ArticleDOI
Potential roles of gut microbiome and metabolites in modulating ALS in mice
Eran Blacher,Stavros Bashiardes,Hagit Shapiro,Daphna Rothschild,Uria Mor,Mally Dori-Bachash,Christian Kleimeyer,Claudia Moresi,Yotam Harnik,Maya Zur,Michal Zabari,Rotem Ben-Zeev Brik,Denise Kviatcovsky,Niv Zmora,Yotam Cohen,Noam Bar,Izhak Levi,Nira Amar,Tevie Mehlman,Alexander Brandis,Inbal E. Biton,Yael Kuperman,Michael Tsoory,Leenor Alfahel,Alon Harmelin,Michal Schwartz,Adrian Israelson,Liisa Arike,Malin E. V. Johansson,Gunnar C. Hansson,Marc Gotkine,Eran Segal,Eran Elinav +32 more
TL;DR: It is demonstrated that Akkermansia muciniphila (AM) ameliorates whereas Ruminococcus torques and Parabacteroides distasonis exacerbate the symptoms of ALS, and it is suggested that environmentally driven microbiome–brain interactions may modulate ALS in mice.
Journal ArticleDOI
Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota
Dae Wook Kang,Dae Wook Kang,James B. Adams,Devon M. Coleman,Elena L. Pollard,Juan Maldonado,Sharon McDonough-Means,J. Gregory Caporaso,Rosa Krajmalnik-Brown +8 more
TL;DR: The observations demonstrate the long-term safety and efficacy of MTT as a potential therapy to treat children with ASD who have GI problems, and warrant a double-blind, placebo-controlled trial in the future.
Journal ArticleDOI
A review of methods and databases for metagenomic classification and assembly.
TL;DR: Two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly are surveyed, and some of the challenges facing these methods are reviewed.
Journal ArticleDOI
Human postprandial responses to food and potential for precision nutrition.
Sarah Berry,Ana M. Valdes,David A. Drew,Francesco Asnicar,Mohsen Mazidi,Jonathan Wolf,Joan Capdevila,George Hadjigeorgiou,Richard Davies,Haya Al Khatib,Christopher Bonnett,Sajaysurya Ganesh,Elco Bakker,Deborah J. Hart,Massimo Mangino,Jordi Merino,Inbar Linenberg,Patrick Wyatt,Jose M. Ordovas,Jose M. Ordovas,Christopher D. Gardner,Linda M. Delahanty,Andrew T. Chan,Nicola Segata,Paul W. Franks,Paul W. Franks,Paul W. Franks,Tim D. Spector +27 more
TL;DR: The PREDICT 1 trial shows large inter-individual variations in postprandial metabolic responses to standardized meals in over 1,000 participants, demonstrating potential for development of personalized nutrition strategies.
Journal ArticleDOI
The role of multiple global change factors in driving soil functions and microbial biodiversity.
Matthias C. Rillig,Masahiro Ryo,Anika Lehmann,Carlos A. Aguilar-Trigueros,Sabine Buchert,Anja Wulf,Aiko Iwasaki,Julien Roy,Gaowen Yang +8 more
TL;DR: It is shown experimentally that increasing the number of simultaneous global change factors caused increasing directional changes in soil properties, soil processes, and microbial communities, though there was greater uncertainty in predicting the magnitude of change.
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.
Journal ArticleDOI
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss,Patrick D. Schloss,Sarah L. Westcott,Sarah L. Westcott,Thomas Ryabin,Justine R. Hall,Martin Hartmann,Emily B. Hollister,Ryan A. Lesniewski,Brian B. Oakley,Donovan H. Parks,Courtney J. Robinson,Jason W. Sahl,Blaz Stres,Gerhard G. Thallinger,David J. Van Horn,Carolyn F. Weber +16 more
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Journal ArticleDOI
UCHIME improves sensitivity and speed of chimera detection
TL;DR: UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences, and in testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus.
Journal ArticleDOI
UPARSE: highly accurate OTU sequences from microbial amplicon reads
TL;DR: The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% correct bases commonly reported by other methods.
Journal ArticleDOI
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
TL;DR: 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.
Related Papers (5)
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
Paul J. McMurdie,Susan Holmes +1 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