Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar) intended for river stocking

Microbiomes play an essential role in promoting host health and fitness in fishes, but the factors driving variation in gut microbiomes among individuals are not fully recognized. Understanding the biological and environmental factors influencing variation in the gut microbiome in fishes is needed to link microbiome composition to host physiology and potentially design manipulations to improve rearing success in fisheries and aquaculture. In this study, we characterized the gut microbiomes of Atlantic salmon (Salmo salar), a globally important species in commercial aquaculture and recreational fishing, considering life stage, vaccination status, and hatchery origin. Microbiomes diverged between hatchery sub-adults (age-0 parrs) and wild adults, with sub-adults exhibiting higher diversity and more similar microbiome communities when compared to adults. The diversity and composition of gut microbiomes did not differ between groups of adults that were reared in two different hatcheries and sampled from the wild. We also found that oral vaccines against bacterial kidney disease (BKD) reduced gut microbial diversity within individual sub-adult salmon, driving increased differentiation of gut microbial communities among individuals. Unvaccinated sub-adults displayed a stable core gut microbiome that was greatly reduced upon vaccination for BKD. Our results suggest that life stage is an essential factor shaping the gut microbiome of Atlantic salmon, likely driven by differences in habitat and diet, and that BKD vaccination can lead to a rapid disruption of the gut microbiome. Conditions experienced in the hatchery environment appear to have a strong influence on host gut microbiomes, but differences at early life stages may be lost due to environmental factors experienced in the wild. The plasticity of the gut microbiome throughout the life of individuals may have important implications for understanding host health, with potential applications for improving the rearing and reintroduction success of the ecologically and economically important Atlantic salmon.