Abstract
Summary Phylogenetic comparative methods are powerful but presently under-utilized ways to identify microbial genes underlying differences in community composition. These methods help to identify functionally important genes because they test for associations beyond those expected when related microbes occupy similar environments. We present phylogenize, a pipeline with web, QIIME2, and R interfaces that allows researchers to perform phylogenetic regression on 16S amplicon and shotgun sequencing data and to visualize results. phylogenize applies broadly to both host-associated and environmental microbiomes. Using Human Microbiome Project and Earth Microbiome Project data, we show that phylogenize draws similar conclusions from 16S versus shotgun sequencing and reveals both known and candidate pathways associated with host colonization.
Availability phylogenize is available at https://phylogenize.org and https://bitbucket.org/pbradz/phylogenize.
Contact kpollard{at}gladstone.ucsf.edu
Footnotes
Rewritten to emphasize differences from previous approaches, to reflect changes in the codebase (now available as an R package and through a QIIME2 plugin as well as through the website) and to add a new analysis of plant rhizosphere-associated microbes; Figure 1 revised; Supplemental file added.
