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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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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Unraveling the Composition of the Root-Associated Bacterial Microbiota of Phragmites australis and Typha latifolia.
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Babajide Ojo,Guadalupe Davila El-Rassi,Mark E. Payton,Penelope Perkins-Veazie,Stephen L. Clarke,Brenda J. Smith,Edralin A. Lucas +6 more
TL;DR: The addition of mango to an HF diet modulated the gut microbiota and production of SCFAs in C57BL/6 mice; these changes may improve gut tolerance to the insult of anHF diet.
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Chloroplast sequence variation and the efficacy of peptide nucleic acids for blocking host amplification in plant microbiome studies
Connor R. Fitzpatrick,Patricia Lu-Irving,Julia K. Copeland,David S. Guttman,Pauline W. Wang,David A. Baltrus,Katrina M. Dlugosch,Marc T. J. Johnson +7 more
TL;DR: A validated framework to modify universal PNA clamps to accommodate host variation in organellar sequences is provided, and it is found that pPNA type had no effect on the detection of individual bacterial taxa, or estimates of within and between sample bacterial diversity, suggesting that the modification did not introduce bias against particular bacterial lineages.
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TL;DR: Generally applicable ecological indices for the statistical analysis of microbial community composition and dynamics based on fingerprinting and NGS datasets are presented warranting interstudy comparability and intuitive interpretability.
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Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi
Valeria Ventorino,Alberto Pascale,Paola Adamo,Claudia Rocco,Nunzio Fiorentino,Mauro Mori,Vincenza Faraco,Olimpia Pepe,Massimo Fagnano +8 more
TL;DR: Investigation of the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin.
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