Genotypic characterization of gut isolates from Atlantic salmon fry reveals beneficial microbes with biotechnological potential.

Aquaculture is a rapidly growing industry, with Atlantic salmon being one of the most intensively farmed food-producing fish in the world. While the gut microbiota is recognized to play an important role in the health and performance of various fish, knowledge of its functional capacities in salmon is gradually expanding, facilitating a better understanding of host-microbiome interactions. Nevertheless, data on the gut microbiota of juvenile salmon remain limited. Here, we isolated and genotypically characterized 11 bacteria obtained from the gut content of Atlantic salmon fry. Whole-genome sequencing using long-read Nanopore technology and functional annotation revealed their extensive metabolic versatility, including a broad array of carbohydrate-active enzymes, proteases, lipases, and (poly)phenol-degrading enzymes potentially contributing to the metabolism of feed-derived components. Additionally, all isolates possessed genomic potential for producing beneficial metabolites, including the short-chain fatty acids acetate and propionate, as well as several B vitamins and vitamin K2. Genes encoding bacteriocins and other secondary metabolites were identified, suggesting niche competitiveness against intestinal pathogens. Among the isolates, we further show that