phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
Paul J. McMurdie,Susan Holmes +1 more
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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
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Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug
Hao Wu,Eduardo Esteve,Eduardo Esteve,Valentina Tremaroli,Muhammad Tanweer Khan,Robert Caesar,Louise Mannerås-Holm,Marcus Ståhlman,Lisa M. Olsson,Matteo Serino,Mercè Planas-Fèlix,Gemma Xifra,Gemma Xifra,Josep M. Mercader,David Torrents,David Torrents,Rémy Burcelin,Rémy Burcelin,Wifredo Ricart,Wifredo Ricart,Rosie Perkins,José Manuel Fernández-Real,José Manuel Fernández-Real,Fredrik Bäckhed,Fredrik Bäckhed,Fredrik Bäckhed +25 more
TL;DR: It is shown that metformin affected pathways with common biological functions in species from two different phyla, and many of the met formin-regulated genes in these species encoded metalloproteins or metal transporters, which provides support for the notion that altered gut microbiota mediates some of metformIn's antidiabetic effects.
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MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data.
TL;DR: This work introduces MicrobiomeAnalyst, a user-friendly tool that integrates recent progress in statistics and visualization techniques, coupled with novel knowledge bases, to enable comprehensive analysis of common data outputs produced from microbiome studies.
Journal ArticleDOI
The neuroactive potential of the human gut microbiota in quality of life and depression
Mireia Valles-Colomer,Mireia Valles-Colomer,Gwen Falony,Gwen Falony,Youssef Darzi,Youssef Darzi,Ettje F. Tigchelaar,Jun Wang,Jun Wang,Raul Y. Tito,Raul Y. Tito,Raul Y. Tito,Carmen Schiweck,Alexander Kurilshikov,Marie Joossens,Marie Joossens,Cisca Wijmenga,Cisca Wijmenga,Stephan Claes,Lukas Van Oudenhove,Alexandra Zhernakova,Sara Vieira-Silva,Sara Vieira-Silva,Jeroen Raes,Jeroen Raes +24 more
TL;DR: Correlation of microbiome features with host quality of life and depression identified specific taxa and microbial pathways in two independent, large population cohorts, identifying links between microbial neuroactive potential and depression.
Journal ArticleDOI
Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data.
TL;DR: This protocol details MicrobiomeAnalyst, a user-friendly, web-based platform for comprehensive statistical, functional, and meta-analysis of microbiome data, a one-stop shop that enables microbiome researchers to thoroughly explore their preprocessed microbiome data via intuitive web interfaces.
Journal ArticleDOI
Temporal and spatial variation of the human microbiota during pregnancy
Daniel B. DiGiulio,Benjamin J. Callahan,Paul J. McMurdie,Elizabeth K. Costello,Deirdre J. Lyell,Anna Robaczewska,Christine L. Sun,Daniela S. Aliaga Goltsman,Ronald J. Wong,Gary M. Shaw,David K. Stevenson,Susan Holmes,David A. Relman +12 more
TL;DR: It is suggested that pregnancy outcomes might be predicted by features of the microbiota early in gestation, as well as the potential impact of a persistent, altered postpartum microbiota on maternal health, including outcomes of pregnancies following short interpregnancy intervals.
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