Ecological dynamics of the Atlantic salmon gut microbiota across developmental phases and geographic regions

The gut microbiota is vital to host health, yet the relative influence of host traits and environmental factors on fish gut microbiota dynamics remains underexplored. We investigated the ecological dynamics of Atlantic salmon (Salmo salar) gut microbiota by analysing 847 samples from wild and farmed salmon across diverse geographic regions, developmental phases, and associated diet and environmental microbiota. Farmed salmon exhibited reduced microbial diversity and distinct community composition with increased Bacillota and reduced Pseudomonadota compared to wild salmon. Microbial diversity declined with advancing developmental phases notably due to reduced Pseudomonadota and expanded Mycoplasma. Diet was the primary contributor (~ 23%) to farmed salmon microbiota, with environmental inputs varying by region and phase. These findings highlight the importance of aquaculture practices guided by microbiota insights, while emphasize the need to preserve microbial diversity in wild populations to enhance resilience against environmental pressures, contributing to both sustainable farming and conservation strategies. Atlantic salmon gut microbiota shows reduced diversity in farmed fish, developmental-stage shifts marked by declining microbial diversity, and major effects of diet and region on farmed salmon microbiota.