Abstract
Summary: Microbes differ in prevalence across environments, but in most cases the causes remain opaque. Phylogenetic comparative methods have emerged as powerful, specific methods to identify microbial genes underlying differences in community composition. However, to apply these methods currently requires computational expertise and sequenced isolates or shotgun metagenomes, limiting their wider adoption. We present phylogenize, a web server that allows researchers to apply phylogenetic regression to 16S amplicon as well as shotgun sequencing data and to visualize results. Using data from the Human Microbiome Project, we show that phylogenize draws similar conclusions from 16S and from shotgun sequencing. Additionally, we apply phylogenize to 16S data from the Earth Microbiome Project, revealing both known and candidate pathways involved in plant colonization. phylogenize has broad applicability to the analysis of both human-associated and environmental microbiomes.
Availability phylogenize is available at https://phylogenize.org with source code available at https://bitbucket.org/pbradz/phylogenize.
Contact kpollard{at}gladstone.ucsf.edu
