PhyloSift: phylogenetic analysis of genomes and metagenomes

Aaron E Darling,Frederick A Matsen,Eric Lowe,Jonathan A Eisen,Guillaume Jospin,Holly M Bik

doi:10.7717/peerj.243

Aaron E Darling, Frederick A Matsen + Show 4 more

Open Access

https://doi.org/10.7717/peerj.243

Copy DOI

Abstract

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).

Highlights

Metagenomics – the sequencing of DNA isolated directly from the environment – has become a routinely used tool with wide applications (Thomas, Gilbert & Meyer, 2012)
As the focus of our current work is on phylogenetic analysis rather than taxonomic classification, we do not discuss the relative merits of each approach to taxonomic classification in detail, nor do we provide benchmarks of taxonomic classification methods
Bayesian hypothesis testing for the presence of phylogenetic lineages For various applications a practitioner might want to test for the presence of a particular lineage of interest in a metagenomic sample

Summary

Introduction

Metagenomics – the sequencing of DNA isolated directly from the environment – has become a routinely used tool with wide applications (Thomas, Gilbert & Meyer, 2012). Used primarily in the study of microorganisms, metagenome sequencing has been carried out on a variety of environments where one finds microbes — from plants and animals to every kind of natural and man-made environment around the globe. How to cite this article Darling et al (2014), PhyloSift: phylogenetic analysis of genomes and metagenomes. Metagenomic sequencing has provided fundamental insight into the diversity of microbes and their function and roles in ecosystems. Due to decreases in the cost and the difficulty of sequencing, metagenomics has become a tool for studying any microbial community, regardless of cultivability

Methods

Results

Conclusion