Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets.

Journal Article (Journal Article)

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 the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen.

Full Text

Duke Authors

Cited Authors

  • Washburne, AD; Silverman, JD; Leff, JW; Bennett, DJ; Darcy, JL; Mukherjee, S; Fierer, N; David, LA

Published Date

  • 2017

Published In

Volume / Issue

  • 5 /

Start / End Page

  • e2969 -

PubMed ID

  • 28289558

Pubmed Central ID

  • PMC5345826

International Standard Serial Number (ISSN)

  • 2167-8359

Digital Object Identifier (DOI)

  • 10.7717/peerj.2969


  • eng

Conference Location

  • United States