Phenotypic and genotypic charcterization of Atlantic Salmon (Salmo salar) gut microbiota

Abstract

Knowledge of the Atlantic Salmon (Salmo salar) gut microbiota falls behind the research done about the human gut microbiome. Creating greater understanding of the bacteria present and their capabilities helps to create a more sustainable aquaculture industry by increasing the possibilities of creating better fish health and farming efficiency. This thesis aims to make a characterization of the gut bacteria using a culturomic based approach using 16S rRNA analysis with Sanger sequencing and Oxford Nanopore sequencing for whole genome analysis in the aim of building upon the Salmon Microbial Genome Atlas (SMGA). Samples was taken from the distal tract of the fish was plated onto different media and the best two media with the best growth was chosen for further work. 56 (34 BHI/22TSA) isolates were chosen for Sanger sequencing, while 45 isolates were processed further for ONT sequencing using the Promethion sequencer. The gut microbiota was dominated by the Pseudomonadota phylum, with smaller quantities of Bacillota and Actinomycetota, while Lelliotta showed the most frequent hits on Genus level. These isolates showed predicted functionality for basic polysaccharide degradation like chitin and acetate for SCFA synthesis, with multiple hits for beta-mannan degrading enzymes.