Metagenomic biomarker discovery and explanation
Nicola Segata,Jacques Izard,Jacques Izard,Levi Waldron,Dirk Gevers,Larisa Miropolsky,Wendy S. Garrett,Curtis Huttenhower +7 more
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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
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Impaired Gut-Liver-Brain Axis in Patients with Cirrhosis
Vishwadeep Ahluwalia,Naga S. Betrapally,Phillip B. Hylemon,Melanie B. White,Patrick M. Gillevet,Ariel Unser,Andrew Fagan,Kalyani Daita,Douglas M. Heuman,Huiping Zhou,Masoumeh Sikaroodi,Jasmohan S. Bajaj +11 more
TL;DR: It is concluded that specific gut microbial taxa are related to neuronal and astrocytic consequences of cirrhosis-associated brain dysfunction.
Journal ArticleDOI
Gut Bacteria Composition Drives Primary Resistance to Cancer Immunotherapy in Renal Cell Carcinoma Patients
Lisa Derosa,Bertrand Routy,Marine Fidelle,Valerio Iebba,Valerio Iebba,Laurie Alla,Edoardo Pasolli,Nicola Segata,Aude Desnoyer,Aude Desnoyer,Filippo Pietrantonio,Gladys Ferrere,Gladys Ferrere,Jean-Eudes Fahrner,Emmanuelle Le Chatellier,Nicolas Pons,Nathalie Galleron,Hugo Roume,Connie P.M. Duong,Connie P.M. Duong,Laura Mondragón,Laura Mondragón,Laura Mondragón,Kristina Iribarren,Mélodie Bonvalet,Mélodie Bonvalet,Safae Terrisse,Conrad Rauber,Conrad Rauber,Conrad Rauber,Anne-Gaëlle Goubet,Anne-Gaëlle Goubet,Anne-Gaëlle Goubet,Romain Daillère,Fabien Lemaitre,Anna Reni,Anna Reni,Beatrice Casu,Beatrice Casu,Maryam Tidjani Alou,Maryam Tidjani Alou,Carolina Alves Costa Silva,Carolina Alves Costa Silva,Didier Raoult,Karim Fizazi,Bernard Escudier,Guido Kroemer,Laurence Albiges,Laurence Albiges,Laurence Zitvogel +49 more
TL;DR: The composition of the microbiota is influenced by TKIs and ATBs, and impacts the success of immunotherapy, and future studies will help sharpen the role of these specific bacteria and their potential as new biomarkers.
Journal ArticleDOI
Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection
Monica Di Paola,Cristina Sani,Ann Maria Clemente,Anna Iossa,Eloisa Perissi,Giuseppe Castronovo,Michele Tanturli,Damariz Rivero,Federico Cozzolino,Duccio Cavalieri,Francesca Carozzi,Carlotta De Filippo,Maria Torcia +12 more
TL;DR: Changes in cervico-vaginal microbiota with Lactobacillus depletion and increased microbial diversity facilitate human papillomavirus (HPV) infection and might be involved in viral persistence and cancer development.
Journal ArticleDOI
Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome.
Ece Mutlu,Işın Y. Comba,Takugo Cho,Phillip A. Engen,Cemal Yazici,Saul Soberanes,Robert B. Hamanaka,Recep Nigdelioglu,Angelo Y. Meliton,Andrew J. Ghio,G. R. Scott Budinger,Gökhan M. Mutlu +11 more
TL;DR: PM-induced alterations in the microbiota were very apparent in beta-diversity comparisons throughout the GI tract and appeared to increase from the proximal to distal parts and maybe a potential mechanism that explains PM induced inflammation in theGI tract.
Journal ArticleDOI
Comparative Microbiome Signatures and Short-Chain Fatty Acids in Mouse, Rat, Non-human Primate, and Human Feces.
Ravinder Nagpal,Shaohua Wang,Leah C. Solberg Woods,Osborne Seshie,Stephanie T. Chung,Carol A. Shively,Thomas C. Register,Suzanne Craft,Donald A. McClain,Hariom Yadav +9 more
TL;DR: These data of host species-specific gut microbiota signatures in some of the most widely used animal models in context to the human microbiota might reflect disparities in host factors, e.g., diets, genetic origin, gender and age, and hence call for prospective studies investigating the features of gut microbiome in such animal models by controlling for these host elements.
References
More filters
Journal ArticleDOI
Matplotlib: A 2D Graphics Environment
TL;DR: Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.
BookDOI
Modern Applied Statistics with S
W. N. Venables,Brian D. Ripley +1 more
TL;DR: A guide to using S environments to perform statistical analyses providing both an introduction to the use of S and a course in modern statistical methods.
Book
Principal Component Analysis
TL;DR: In this article, the authors present a graphical representation of data using Principal Component Analysis (PCA) for time series and other non-independent data, as well as a generalization and adaptation of principal component analysis.
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
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
TL;DR: The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
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