MPASS

MPASS compares whole protein-coding gene content across metagenomic shotgun sequencing datasets to infer phylogenetic relationships among microbial communities and relate those relationships to environmental factors.

Key Features:

• Whole Proteome Comparison: Compares whole proteomes deduced from metagenomic shotgun sequencing data to quantify similarity among samples.
• Phylogenetic Tree Construction: Constructs metagenomic phylogenetic trees based on average sequence similarity of protein-coding genes.
• Environmental Correlation Analysis: Compares metagenomic trees with dendrograms of environmental factors to identify environmental influences on community composition.
• Validation and Application: Validated using simulated metagenomes and real-world samples from soil, water, and Kirishima hot springs in Japan.
• Taxonomic and Functional Insights: Reflects microbiota dynamics at both taxonomic and functional levels to provide multi-dimensional ecosystem perspectives.

Scientific Applications:

• Community assembly analysis: Elucidates principles governing microbial community establishment from metagenomic data.
• Environmental driver identification: Identifies environmental factors that drive changes in microbiota composition.
• Environmental gradient studies: Assesses the impact of environmental gradients on microbial diversity and function.
• Quantitative metagenomic framework: Provides a quantitative framework integrating phylogenetic data with environmental variables for ecological studies.

Methodology:

MPASS deduces proteomes from metagenomic shotgun sequencing data and constructs phylogenetic trees based on average sequence similarity of protein-coding genes.