Ecological strategies of bacteria shape inherent phage diversity in Atlantic salmon gut microbiomes

Understanding host-specific phage diversity is essential for deciphering the complex dynamics shaping microbial ecology and evolution. However, the lack of inherent host associations between uncultivated bacteria and their viruses remains a major limitation to understanding the drivers of viral diversity and its role in bacterial ecology, particularly given the intricate specificity of phage-host interactions. The naturally low complexity of the gut microbiota within piscivorous fish, such as Atlantic salmon (<i>Salmo salar</i>), makes it a valuable model for unravelling ecological patterns of viral diversity in the context of a limited bacterial species composition, and to explore the impact of an invading pathogen on the ‘steady-state’ viral community. The intestinal microbiota of the salmon studied here, was in some cases dominated by a salmon-associated <i>Mycoplasma</i> or increasing levels of an opportunistic <i>Aliivibrio,</i> the latter observed in response to a disease outbreak. The two bacteria are distinctively different in their ecological strategies and their overall genomic and functional properties. A pronounced difference was observed in the gut viral communities and diversity, depending on whether it was dominated by a commensal or an invading bacterial species. Samples dominated by <i>Mycoplasma</i> sp. had few to no viruses, whereas samples dominated by <i>Aliivibrio</i> sp. had viral communities comprising up to 22 viral taxonomic operational units. This study provides unique insights into the significance of bacterial ecological trade-offs linked to niche adaptation and how these affect the associated viral communities in a natural host-controlled environment.