Microbiomes play an essential role in promoting host health and fitness, but the factors affecting variation in gut microbiomes among individuals are not fully understood. Investigating the microbiome under different conditions is needed to link gut microbiomes to host physiology and potentially design manipulations to improve rearing success of captive species. In this study, we characterized the gut microbiomes of Atlantic salmon (Salmo salar) in individuals at different life stages, vaccination status, and hatchery origin. Microbiomes differed between age-0 sub-adults and adults, with sub-adults exhibiting higher diversity and more similar communities when compared to adults. We also found that vaccines against bacterial kidney disease reduced gut microbial diversity within individual sub-adult salmon, resulting in dissimilar gut microbial communities among individuals. The diversity and structure of microbiomes did not differ between groups of adults that were reared in two different hatcheries and sampled from the wild. Sub-adults, particularly unvaccinated sub-adults, displayed a strong core microbiome present in the majority of individuals. Our results suggest that life stage and vaccination status are essential factors in the gut microbiome development of salmon. Conditions experienced during early life stages appear to have a strong influence on the microbiome, but differences among individuals at early life stages may be lost due to environmental factors experienced later in life. The plasticity of the 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.

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