MetaPopR

MetaPopR performs comprehensive analyses and visualization of microbial and viral community metagenomes at both macro- and microdiversity levels.

Key Features:

• Genome-resolved analyses: Combines macro- and microdiversity analyses for genome-resolved studies of microbial and viral communities.
• Macrodiversity analysis: Estimates population abundances and calculates α- and β-diversity metrics.
• Microdiversity calculations: Identifies single nucleotide polymorphisms (SNPs), applies codon-constrained linkage methods, computes nucleotide diversity indices (π and θ), assesses selective pressures via pN/pS ratios and Tajima's D, and evaluates fixation indices (F_ST) between populations.
• Gene identification: Identifies genes with distinct codon usage patterns to reveal genetic architecture within communities.
• Visualization: Generates visualizations of metagenomic macro- and microdiversity results.

Scientific Applications:

• Gut virome analysis in autism and FMT: Applied to gut viromes from autistic children who underwent fecal microbiota transfer (FMT) and neurotypical peers to compare viral population diversity.
• Microdiversity and nucleotide diversity (π): Detected lower average viral nucleotide diversity (π) in autistic children relative to neurotypical peers, indicating reduced intra-population variation.
• Selective pressure assessment: Revealed a lower percentage of genomes under positive selection among autistic children based on pN/pS and Tajima's D analyses.
• FMT delivery method comparisons: Highlighted differences in microdiversity pre- and post-FMT between oral and rectal delivery methods, indicating delivery-dependent effects on viral activity and engraftment.

Methodology:

Identifies SNPs, applies codon-constrained linkage methods, computes nucleotide diversity (π, θ), pN/pS ratios, Tajima's D, and F_ST, estimates population abundances and α/β diversity metrics, identifies genes with distinct codon usage, and generates visualizations.