Prophage Detection and Annotation
One-Sentence Definition
Prophage detection identifies integrated or plasmid-like phage genomes within bacterial assemblies and annotates their cargo — including toxins, virulence factors, and mobility genes.
Simple Explanation
Find the viral DNA hiding inside a bacterium’s genome and check whether it carries toxins or other dangerous extras.
Detailed Scientific Explanation
Approaches: similarity to phage DB (PHASTER, Phigaro, geNomad, VirSorter2), gene content (integrase, terminase, capsid), and genome graph signals.
Cargo of medical importance:
| Prophage cargo | Example |
|---|---|
| Shiga toxin | Stx phages in STEC |
| Diphtheria toxin | Corynebacterium β-phage |
| Cholera toxin | CTXΦ |
| Superantigens | Some staphylococcal phages |
| AMR genes | Occasional; less common than plasmids |
Links to Transduction and Genomic Islands.
Mechanism
Scan assembly for phage-like regions → boundary prediction → annotate structural vs cargo genes → assess intact vs remnant / cryptic status.
Clinical Importance
- Explains toxin-positive pathotypes among otherwise similar E. coli.
- Phage therapy design needs to know resident prophages (immunity, lysogenic conversion).
Research Importance
- Viral dark matter in microbiomes; phage–host coevolution with CRISPR-Cas in Bacteria.
Diagnostic Relevance
- Toxin gene PCR often targets prophage cargo; WGS confirms context.
AMR Relevance
Lower than plasmids overall, but lysogeny can alter fitness and antibiotic stress responses; rare AMR-phage reports exist.
Related Methods
Related MOCs
Active Recall Questions
- Name two toxins encoded on prophages.
- Intact vs cryptic prophage — why care?
- How does CRISPR interact with prophages?