PropagAtE

PropagAtE estimates the activity state (lysogenic versus lytic) of integrated prophages in metagenomic datasets by comparing short-read coverage of prophage genomic coordinates to their host genomes to infer active replication.

Key Features:

• Input data: Uses genomic coordinates of integrated prophage sequences together with short sequencing reads from metagenomic datasets.
• Coverage-based analysis: Computes read coverage ratios between prophage regions and their host genomes to assess relative replication.
• Statistical evaluation: Applies statistical analyses to read coverage comparisons to estimate prophage activity states (lysogenic vs lytic).
• Induction-agnostic detection: Identifies actively replicating prophages irrespective of whether activation was induced externally or occurred spontaneously.
• Sensitivity across depths: Demonstrates sensitivity to detect prophage activity across varying sequencing depths.
• Automated performance: Implements an automated computational approach with reported speed and accuracy for large datasets.

Scientific Applications:

• Metagenomic surveys: Applied to complex metagenomes to reveal spatial and temporal activation patterns of prophages.
• Environmental microbiomes: Identified environment-specific active prophage populations, including Myxococcales in fens, Acetobacteraceae in palsas, and Acidimicrobiaceae in bogs.
• Host-associated microbiomes: Used on murine and human gut metagenomes, showing the highest proportion of active prophages in murine gut and persistent but often inactive prophage populations in the human gut.
• Functional linkage: Associated prophage sequences with encoded genes such as cysH (sulfur metabolism) and rhuM-like virulence factors in human gut prophages.

Methodology:

Uses genomic coordinates of integrated prophage sequences and short sequencing reads, computes read coverage ratios between prophage regions and host genomes, and applies statistical analyses to infer lysogenic versus lytic activity.