Research on Prophages in Aquaculture from the Perspective of Paradigm Borrowing: Advances in Pathogen Virulence, Antimicrobial Resistance, and Environmental Regulation

Prophages are widespread in bacterial genomes and can influence pathogen evolution by modulating virulence, antimicrobial resistance, environmental adaptation, and competitive fitness. However, prophage research in aquaculture pathogens remains limited, with abundant genomic predictions but scarce functional validation, numerous cross-sectional surveys but little longitudinal tracking, and extensive phenomenological observations but insufficient mechanistic investigation. This review synthesizes current knowledge of prophages in aquatic bacterial pathogens, focusing on their roles in virulence, antimicrobial resistance, and competitive advantage, while drawing on mechanistic paradigms established in human and animal pathogens. We further propose a pathogen-centered “molecular bridge” framework in which environmental perturbations alter bacterial physiological states, are interpreted through prophage regulatory mechanisms, and ultimately translate into changes in pathogen phenotypes, fitness, and pathogenic potential. Particular attention is given to multi-signal interactions, induction thresholds, and the context-dependent fitness consequences of prophage induction in dynamic aquaculture environments. Finally, we propose future priorities encompassing systematic prophage resource construction, functional validation, multi-stressor experiments, and longitudinal monitoring. By adopting a paradigm-borrowing review approach, this review aims to provide a transferable roadmap for prophage research in aquaculture, to facilitate translational applications, and to offer theoretical support for precision disease control in aquaculture.