Phylogenetic factorization of compositional data

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, “phylofactorization”, to re-analyze datasets from human body and soil microbial communities, demonstrating how phylofactorization can be a dimensionality-reducing tool, an ordination-visualization tool, and also mass-produce inferences on the edges in the phylogeny in which meaningful differences arose.