PhyloMed: a phylogeny-based test of mediation effect in microbiome

Microbiome data from sequencing experiments contain the relative abundance of a large number of microbial taxa with their evolutionary relationships represented by a phylogenetic tree. The compositional and high-dimensional nature of the microbiome mediator challenges the validity of standard mediation analyses. We propose a phylogeny-based mediation analysis method called PhyloMed to address this challenge. Unlike existing methods that directly identify individual mediating taxa, PhyloMed discovers mediation signals by analyzing subcompositions defined on the phylogenic tree. PhyloMed produces well-calibrated mediation test p-values and yields substantially higher discovery power than existing methods.

Automated summary

PhyloMed is a phylogeny-based mediation analysis method that addresses the challenges of compositional and high-dimensional microbiome data. It discovers mediation signals by analyzing subcompositions defined on the phylogenetic tree, producing well-calibrated mediation test p-values and higher discovery power than existing methods.