Bacteriophage & Mode of Action (MoA)

The gut harbors a large genetic reservoir of integrated prophages (i.e., Gene transfer agents (GTAs) are domesticated prophages) with phage-like traits, including the ability to cause host cell lysis for gene transfer. But the vast majority are either cryptic (inactivated by excision gene mutations) or require specific, biologically relevant triggers - including products of lysed host cells - to replicate. The activity of temperate phages in the gut is far more restricted, context-dependent, and ecologically nuanced than metagenomic studies alone would suggest.
Dahlman et al. 2025 Nature 647: 698-705
Banks et al. 2026 Nat Microbiol 11: 1511-1530

Most prophages (i.e., genomes of a temperate bacteriophage) remained stably integrated into their bacteral h…