Structure of Bacterial Communities in Brown Trout (Salmo trutta L.) at Different Ontogenetic Stages

Abstract This study provides the data on the microbial communities associated with brown trout (Salmo trutta L.) at the yolk-sac stage and within the gut of one-year-old individuals reared in a recirculating aquaculture system (RAS) in the Arkhangelsk region. Taxonomic profiling of bacterial communities in both larvae and adult fish was conducted using metabarcoding of the V4 hypervariable region of the 16S rRNA gene. The results indicate that the yolk-sac stage microbiota is predominantly composed of genera Lactobacillus, Cutibacterium, Polynucleobacter, and members of the family Comamonadaceae, whereas the gut microbiota of adult individuals is dominated by Lactobacillus, Pseudomonas, Acetobacter, and Cutibacterium. Alpha diversity indices (Shannon, Simpson, Chao1) revealed moderate abundance and homogeneity of the microbial communities at the early development stage, with a subsequent increase in microbial diversity and heterogeneity in adults. Beta diversity analysis identified overlapping yet largely distinct communities across the different ontogenetic stages. The core set of metabolically and physiologically significant bacteria appears to be primarily shaped by internal succession and dietary interactions, whereas the contribution of environmental water microbiota is limited. These findings on diversity and composition of the bacterial communities in brown trout offer a foundation for development of probiotic and management strategies in aquaculture aimed at enhancing digestive efficiency, immune competence, and post-release survival in natural water bodies.