LAUSR

Simple Summary The epidermis and epidermal mucus layer of fish function as a first barrier against waterborne pathogens, while also providing niches for symbiotic microorganisms that can be beneficial to the host’s health. Controlling the composition of the fish skin microflora is important in pathogen management in aquaculture; however, our understanding of the characteristics of this microflora is limited. To elucidate the characteristics of fish skin bacterial flora, we examined the epidermal mucous of rainbow trout reared in flow-through aquaculture as an experimental model with environmental perturbations. Our experimental data indicate that some specific bacteria with antimicrobial activity enter from the natural environment and affect compositional changes in the skin mucous bacterial community by disturbing and occupying it. This perturbation by antimicrobial bacteria can “remodel” the fish skin bacterial flora and thereby affect the host′s health. This study provides novel information on factors influencing the composition of fish skin bacterial flora, which is applicable for controlling fish disease by using beneficial bacteria in aquaculture. Abstract The bacterial flora of the epidermal mucus of fish is closely associated with the host’s health and susceptibility to pathogenic infections. In this study, we analyzed the epidermal mucus bacteria of rainbow trout (Oncorhynchus mykiss) reared in flow-through aquaculture under environmental perturbations. Over ~2 years, the bacteria present in the skin mucus and water were analyzed based on the 16S rDNA sequences. The composition of the mucus bacterial community showed significant monthly fluctuations, with frequent changes in the dominant bacterial species. Analysis of the beta- and alpha-diversity of the mucus bacterial flora showed the fluctuations of the composition of the flora were caused by the genera Pseudomonas, Yersinia, and Flavobacterium, and some species of Pseudomonas and Yersinia in the mucus were identified as antimicrobial bacteria. Examination of the antimicrobial bacteria in the lab aquarium showed that the natural presence of antimicrobial bacteria in the mucus and water, or the purposeful addition of them to the rearing water, caused a transition in the mucus bacteria community composition. These results demonstrate that specific antimicrobial bacteria in the water or in epidermal mucus comprise one of the causes of changes in fish epidermal mucus microflora.