From hijackers to architects: the role of prophages in bacterial genome evolution

Prophages, as the integrated or plasmid-like forms of temperate bacteriophage genomes, are critical genetic elements that establish stable interactions with their hosts, profoundly impacting host physiology and ecology. Prophages confer multiple advantages to their hosts. They promote changes in the bacterial genome structure and function—such as rearrangements, introduction of novel genes, and gene expression reprogramming—that often enhance bacterial fitness and persistence. Active prophages influence microbial community dynamics through the lytic-lysogenic cycle alternations, while both active and cryptic prophages modulate host behavior, genomic diversification, and interspecific interactions. Given that lysogeny is ubiquitous in nature, prophages play a pivotal role in shaping bacterial ecological functions and evolutionary trajectories. In this review, we provide a comprehensive overview of phage development and the contribution of prophages as modifiers of genome structure and function. We further discuss the long-term consequences of shaping genome architecture in the context of bacterial ecology and evolution, and propose emerging research directions to advance our understanding of phage-host interactions and their impact on microbial ecosystems.