CoPTR

CoPTR computes peak-to-trough ratios (PTRs) from metagenomic sequencing coverage patterns across bacterial genomes to infer microbial growth rates and characterize host-associated microbial dynamics.

Key Features:

• Accurate PTR Computation: Computes PTRs from complete reference genomes and assemblies to provide comprehensive PTR estimates from metagenomic sequencing data.
• Biological Interpretation: Implements theoretical frameworks that formalize the interpretation of PTRs as measures linked to microbial growth rates.
• High Inter-Individual Variation Detection: Detects significant inter-individual variation in PTR values, demonstrated in a case-control study of 1304 metagenomic samples from individuals with irritable bowel disease.
• Loose Correlation with Relative Abundances: Shows PTRs exhibit only a loose correlation with relative abundances, indicating growth signals distinct from abundance metrics.
• Association with Disease Status: Identifies associations between PTR values and disease status, including irritable bowel disease.
• Integration with Multi-Omics Data: Facilitates integration of PTRs with relative abundances and metabolomics for combined analyses of growth, composition, and metabolic profiles.

Scientific Applications:

• Microbial Ecology: Quantifying growth dynamics within microbial communities using PTR-derived growth estimates.
• Host–Microbe Interactions: Analyzing host-associated microbial growth patterns and dynamics in metagenomic datasets.
• Disease-Associated Microbiome Studies: Investigating microbial growth signatures associated with disease status, exemplified by irritable bowel disease case-control data (1304 metagenomic samples).
• Multi-Omics Integration: Combining PTRs with relative abundances and metabolomics to elucidate relationships between growth rates, community composition, and metabolites.

Methodology:

Computes peak-to-trough ratios (PTRs) by analyzing sequencing coverage patterns along bacterial genomes and assemblies from metagenomic sequencing using a reference database of 2935 species.