PhyloMed

PhyloMed performs phylogeny-based mediation analysis on microbiome sequencing data to assess how microbial subcompositions defined by a phylogenetic tree mediate effects on host phenotypes or environmental exposures.

Key Features:

• Phylogeny-Based Approach: Analyzes subcompositions defined by the phylogenetic tree to leverage evolutionary relationships among microbial taxa.
• Handles Compositional and High-Dimensional Data: Addresses compositional constraints and high dimensionality inherent in microbiome sequencing data.
• Well-Calibrated P-Values: Produces well-calibrated p-values for mediation tests to support statistical reliability and control false discoveries.
• Increased Discovery Power: Demonstrates higher discovery power compared to methods that treat taxa independently.
• Robustness to Data Sparsity: Mitigates issues related to data sparsity in microbiome datasets.

Scientific Applications:

• Host-microbiome mediation studies: Assess how changes in microbial composition mediate effects on human or animal host phenotypes in health research.
• Environmental microbiome studies: Evaluate mediating roles of microbial communities in responses to environmental factors.
• Ecology and evolutionary biology: Explore mediation of ecological and evolutionary processes by microbial community composition.

Methodology:

Integrates phylogenetic information into mediation analysis by focusing on subcompositions within the phylogenetic tree and computing well-calibrated p-values to account for compositionality, high dimensionality, and data sparsity.