phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
Paul J. McMurdie,Susan Holmes +1 more
TLDR
The phyloseq project for R is a new open-source software package dedicated to the object-oriented representation and analysis of microbiome census data in R, which supports importing data from a variety of common formats, as well as many analysis techniques.Abstract:
Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.read more
Citations
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Journal ArticleDOI
Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice
Gil Sharon,Nikki Jamie Cruz,Dae Wook Kang,Michael J. Gandal,B. D. Wang,Young-Mo Kim,Erika M. Zink,Cameron P. Casey,Bryn C. Taylor,Christianne J. Lane,Lisa M. Bramer,Nancy G. Isern,David W. Hoyt,Cecilia Noecker,Michael J. Sweredoski,Annie Moradian,Elhanan Borenstein,Janet K. Jansson,Rob Knight,Thomas O. Metz,Carlos Lois,Daniel H. Geschwind,Rosa Krajmalnik-Brown,Sarkis K. Mazmanian +23 more
TL;DR: It is proposed that the gut microbiota regulates behaviors in mice via production of neuroactive metabolites, suggesting that gut-brain connections contribute to the pathophysiology of ASD.
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Assembly and ecological function of the root microbiome across angiosperm plant species.
Connor R. Fitzpatrick,Julia K. Copeland,Pauline W. Wang,David S. Guttman,Peter M. Kotanen,Marc T. J. Johnson +5 more
TL;DR: It is demonstrated that variation among 30 angiosperm species, which have diverged for up to 140 million years, affects root bacterial diversity and composition and the causes of variation in root microbiomes are emphasized.
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Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
TL;DR: The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome, and that some low-frequency taxa seemingly associated with preterm birth were run-specific contaminants.
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New evidences on the altered gut microbiota in autism spectrum disorders
Francesco Strati,Duccio Cavalieri,Davide Albanese,Claudio De Felice,Claudio Donati,Joussef Hayek,Olivier Jousson,Silvia Leoncini,Daniela Renzi,Antonino Salvatore Calabrò,Carlotta De Filippo +10 more
TL;DR: The finding that, besides the bacterial gut microbiota, also the gut mycobiota contributes to the alteration of the intestinal microbial community structure in ASDs opens the possibility for new potential intervention strategies aimed at the relief of gastrointestinal symptoms in AsDs.
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Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots
Samiran Banerjee,Florian Walder,Lucie Büchi,Marcel Meyer,Alain Y. Held,Andreas Gattinger,Andreas Gattinger,Thomas Keller,Raphaël Charles,Marcel G. A. van der Heijden +9 more
TL;DR: It is demonstrated that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome, and this is the first study to report mycorrhizal keystoneTaxa for agroecosystems.
References
More filters
Journal Article
R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Book
ggplot2: Elegant Graphics for Data Analysis
TL;DR: This book describes ggplot2, a new data visualization package for R that uses the insights from Leland Wilkisons Grammar of Graphics to create a powerful and flexible system for creating data graphics.
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.
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