phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
Paul J. McMurdie,Susan Holmes +1 more
Reads0
Chats0
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
More filters
Journal ArticleDOI
The potential role of vitamin D supplementation as a gut microbiota modifier in healthy individuals.
TL;DR: The positive impact of vitamin D supplementation on the gut microbiota and the potential for the microbial gut signature to affect vitamin D response are highlighted.
Journal ArticleDOI
The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination through a Bile Acid-Type I IFN Signaling Axis
Emma S. Winkler,Swathi Shrihari,Barry L. Hykes,Scott A. Handley,Prabhakar S. Andhey,Yan-Jang S. Huang,Amanda Swain,Lindsay Droit,Kranthi K. Chebrolu,Matthias Mack,Dana L. Vanlandingham,Larissa B. Thackray,Marina Cella,Marco Colonna,Maxim N. Artyomov,Thaddeus S. Stappenbeck,Michael S. Diamond +16 more
TL;DR: It is shown that symbiotic intestinal bacteria modulate antiviral immunity and levels of circulating alphaviruses within hours of infection through a bile acid-pDC-IFN signaling axis, which affects viremia, dissemination, and potentially transmission.
Journal ArticleDOI
Bacterial release from pipe biofilm in a full-scale drinking water distribution system
Sandy Chan,Kristjan Pullerits,Alexander Keucken,Kenneth M Persson,Catherine J. Paul,Peter Rådström +5 more
TL;DR: In this paper, the authors describe the number of cells released from a pipe biofilm, their cellular characteristics, and their identity as they shaped a drinking water microbiome, showing that ultra-filtration at full scale in Varberg, Sweden reduced the total cell count to 1.5% of the cells in the distributed water.
Journal ArticleDOI
Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome
Malte C. Rühlemann,Britt Marie Hermes,Britt Marie Hermes,Britt Marie Hermes,Corinna Bang,Shauni Doms,Shauni Doms,Lucas Moitinho-Silva,Louise B. Thingholm,Fabian Frost,Frauke Degenhardt,Michael Wittig,Jan Christian Kässens,Frank Ulrich Weiss,Annette Peters,Klaus Neuhaus,Uwe Völker,Henry Völzke,Georg Homuth,Stefan Weiss,Harald Grallert,Matthias Laudes,Wolfgang Lieb,Dirk Haller,Markus M. Lerch,John F. Baines,John F. Baines,Andre Franke +27 more
TL;DR: In this article, a genome-wide association analysis of 8,956 German individuals, identified 38 genetic loci to be associated with single bacteria and overall microbiome composition, and further analyses confirm the identified associations of ABO histo-blood groups and FUT2 secretor status with Bacteroides and Faecalibacterium spp.
Journal ArticleDOI
Fetal meconium does not have a detectable microbiota before birth.
Katherine M. Kennedy,Max J. Gerlach,Thomas Adam,Markus M. Heimesaat,Laura Rossi,Michael G. Surette,Deborah M. Sloboda,Thorsten Braun +7 more
TL;DR: In this paper, the authors investigated whether bacteria could be detected in meconium before birth and concluded that fetal colonisation of healthy term infants does not occur before birth, indicating that colonization occurs during and after birth.
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.
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