PhyloSift: phylogenetic analysis of genomes and metagenomes.
Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata. These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454).
ithree institute, University of Technology Sydney , Sydney , Australia ; Genome Center, University of California , Davis, CA , United States of America.
Aaron E
AE
Darling
Genome Center, University of California , Davis, CA , United States of America.
Guillaume
G
Jospin
Genome Center, University of California , Davis, CA , United States of America.
Eric
E
Lowe
Fred Hutchinson Cancer Research Center , Seattle, WA , United States of America.
Frederick A
FA
Matsen
Genome Center, University of California , Davis, CA , United States of America.
Holly M
HM
Bik
Department of Evolution and Ecology, University of California , Davis, CA , United States of America ; Department of Medical Microbiology and Immunology, University of California , Davis, CA , United States of America.
Jonathan A
JA
Eisen
Bayes factor; Community structure; Edge PCA; Forensics; Metagenomics; Microbial diversity; Microbial ecology; Microbial evolution; Phylogenetic diversity; Phylogenetics