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

## TL;DR

This study identifies beneficial gut bacteria in Atlantic salmon fry that could improve feed digestibility and fish health.

## Contribution

The study provides novel insights into the functional potential of gut bacteria in salmon fry, including a specific isolate that can break down anti-nutritional oligosaccharides.

## Key findings

- Eleven gut bacteria isolates from salmon fry were found to have diverse metabolic capabilities, including carbohydrate and lipid metabolism.
- Lactococcus raffinolactis ASF-5 can degrade raffinose, an anti-nutritional compound in plant-based feeds, using specific glycoside hydrolases.
- The isolates showed genomic potential to produce beneficial metabolites like short-chain fatty acids, vitamins, and bacteriocins.

## Abstract

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 Lactococcus raffinolactis ASF-5 has the potential to selectively remove indigestible oligosaccharides from plant-based feeds. Indeed, this isolate grew on raffinose, an oligosaccharide associated with anti-nutritional effects in salmon. Using AlphaFold 3 models, we show that this capability is supported by a GH36 α-galactosidase and two GH32 sucrases, which can act cooperatively in the complete hydrolysis of raffinose. Finally, L. raffinolactis ASF-5 had a favorable safety profile for use as a feed supplement, showing susceptibility to all tested antibiotics and lacking hemolytic activity.

Although metataxonomy studies have enhanced our knowledge of the salmon gut microbiota, the functional potential of bacteria from this ecosystem remains underexplored. Well-characterized bacterial isolates are crucial to advance the growing salmon aquaculture field, allowing insights into nutrient metabolism, informing the development of beneficial interventions, and helping in identifying enzymes to improve feed digestibility. This study highlights the functional capacity of 11 bacteria isolated from the gut of salmon fry in contributing to the metabolism of carbohydrates, proteins, lipids, fatty acids, and (poly)phenols from feed, potentially increasing nutrient availability for the host or providing beneficial metabolites, including short-chain fatty acids, vitamins, and bacteriocins. Importantly, Lactococcus raffinolactis ASF-5 could be used to remove indigestible sugars like raffinose from plant meals. Identifying such beneficial, host-specific bacteria opens new opportunities for developing customized feed supplements or enzymes that enhance feed digestibility, to promote the health and welfare of Atlantic salmon, and enhance the economic sustainability of aquaculture.