Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +7 more
Reads0
Chats0
TLDR
A new method for metagenomic biomarker discovery is described and validates by way of class comparison, tests of biological consistency and effect size estimation to address the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.Abstract:
This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.read more
Citations
More filters
Journal ArticleDOI
Diet rapidly and reproducibly alters the human gut microbiome
Lawrence A. David,Corinne F. Maurice,Rachel N. Carmody,David B. Gootenberg,Julie E. Button,Benjamin E. Wolfe,Alisha V. Ling,A. Sloan Devlin,Yug Varma,Michael A. Fischbach,Sudha B. Biddinger,Rachel J. Dutton,Peter J. Turnbaugh +12 more
TL;DR: Increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease.
Journal ArticleDOI
Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +6 more
TL;DR: In this article, a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation is described and validated, which addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.
Journal ArticleDOI
Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients
Vancheswaran Gopalakrishnan,Vancheswaran Gopalakrishnan,Christine N. Spencer,Christine N. Spencer,Luigi Nezi,Alexandre Reuben,Miles C. Andrews,Tatiana Karpinets,Peter A. Prieto,D. Vicente,K. Hoffman,Spencer C. Wei,Alexandria P. Cogdill,Li Zhao,Courtney W. Hudgens,Diane S. Hutchinson,T. Manzo,M. Petaccia de Macedo,Tiziana Cotechini,T. Kumar,Wei Shen Chen,Sangeetha M. Reddy,R. Szczepaniak Sloane,Jessica Galloway-Peña,Hong Jiang,P. L. Chen,Elizabeth J. Shpall,Katayoun Rezvani,Amin M. Alousi,Roy F. Chemaly,Samuel A. Shelburne,Luis M Vence,Pablo C. Okhuysen,V. B. Jensen,Alton G. Swennes,Florencia McAllister,E. Marcelo Riquelme Sanchez,Yu Zhang,Laurence Zitvogel,Nicolas Pons,Jacob Austin-Breneman,Lauren E. Haydu,Elizabeth M. Burton,J. M. Gardner,E. Sirmans,Jing Shan Hu,Alexander J. Lazar,Takahiro Tsujikawa,Adi Diab,Hussein Abdul-Hassan Tawbi,Isabella C. Glitza,Wen-Jen Hwu,Sapna Pradyuman Patel,Scott E. Woodman,Rodabe N. Amaria,Michael A. Davies,Jeffrey E. Gershenwald,Patrick Hwu,J. E. Lee,Jianhua Zhang,Lisa M. Coussens,Zachary A. Cooper,P.A. Futreal,Carrie R. Daniel,Carrie R. Daniel,Nadim J. Ajami,Joseph F. Petrosino,Michael T. Tetzlaff,Pradeep Sharma,James P. Allison,Robert R. Jenq,Jennifer A. Wargo +71 more
TL;DR: Examination of the oral and gut microbiome of melanoma patients undergoing anti-programmed cell death 1 protein (PD-1) immunotherapy suggested enhanced systemic and antitumor immunity in responding patients with a favorable gut microbiome as well as in germ-free mice receiving fecal transplants from responding patients.
Journal ArticleDOI
Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders
Elaine Y. Hsiao,Sara Mcbride,Sophia Hsien,Gil Sharon,Embriette R. Hyde,Tyler McCue,Julian A. Codelli,Janet Chow,Sarah E. Reisman,Joseph F. Petrosino,Paul H. Patterson,Sarkis K. Mazmanian +11 more
TL;DR: A gut-microbiome-brain connection in a mouse model of ASD is supported and a potential probiotic therapy for GI and particular behavioral symptoms in human neurodevelopmental disorders is identified.
Journal ArticleDOI
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
Xochitl C. Morgan,Timothy L. Tickle,Timothy L. Tickle,Harry Sokol,Harry Sokol,Dirk Gevers,Kathryn L. Devaney,Doyle V. Ward,Joshua A Reyes,Samir A. Shah,Neal Leleiko,Scott B. Snapper,Athos Bousvaros,Joshua R. Korzenik,Joshua R. Korzenik,Bruce E. Sands,Ramnik J. Xavier,Ramnik J. Xavier,Curtis Huttenhower,Curtis Huttenhower +19 more
TL;DR: The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways, and the first insights into community-wide microbial processes and pathways that underpin IBD pathogenesis are provided.
References
More filters
Journal ArticleDOI
The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes
Folker Meyer,Folker Meyer,Daniel Paarmann,Mark D'Souza,Robert Olson,Elizabeth M. Glass,Michael Kubal,Tobias Paczian,Alexis A. Rodriguez,Rick Stevens,Rick Stevens,Andreas Wilke,Jared Wilkening,Robert Edwards,Robert Edwards +14 more
TL;DR: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes that is stable, extensible, and freely available to all researchers.
Journal ArticleDOI
Use of proteomic patterns in serum to identify ovarian cancer
Emanuel F. Petricoin,Ali M. Ardekani,Ben A. Hitt,Peter J. Levine,Vincent A. Fusaro,Seth M. Steinberg,Gordon B. Mills,Charles B. Simone,David A. Fishman,Elise C. Kohn,Lance A. Liotta +10 more
TL;DR: A bioinformatics tool was developed and used to identify proteomic patterns in serum that distinguish neoplastic from non-neoplastic disease within the ovary, justifying a prospective population-based assessment of proteomic pattern technology as a screening tool for all stages of ovarian cancer in high-risk and general populations.
Journal ArticleDOI
Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +6 more
TL;DR: In this article, a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation is described and validated, which addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities.
Journal ArticleDOI
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
Brian J. Haas,Dirk Gevers,Ashlee M. Earl,Mike Feldgarden,Doyle V. Ward,Georgia Giannoukos,Dawn Ciulla,Diana Tabbaa,Sarah K. Highlander,Erica Sodergren,Barbara A. Methé,Todd Z. DeSantis,Joseph F. Petrosino,Rob Knight,Bruce W. Birren +14 more
TL;DR: A new chimera detection tool called Chimera Slayer (CS), which detects chimeras with greater sensitivity than previous methods, performs well on short sequences such as those produced by the 454 Life Sciences (Roche) Genome Sequencer, and can scale to large data sets.
Journal ArticleDOI
Ecological and evolutionary forces shaping microbial diversity in the human intestine.
TL;DR: The human gut is populated with as many as 100 trillion cells, whose collective genome, the microbiome, is a reflection of evolutionary selection pressures acting at the level of the host and at thelevel of the microbial cell.
Related Papers (5)
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
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