Effects of microbe- and mussel-based diets on the gut microbiota in Arctic charr (Salvelinus alpinus)

A major challenge in aquaculture is finding nutrient resources that do not compete with human demandand do not threaten ecological sustainability. Single cell proteins, such as filamentous fungi and yeasts,have similar nutrient profiles to fish meal, grow fast under optimal conditions and contain high amountsof protein, making them attractive candidates as alternative nutrient sources for farmed fish. Moreover,the cell walls of yeasts and filamentous fungi have bioactive properties, potentially mediated via theintestinal microbiota, that positively affect the intestinal health of fish. The microbiota in fish is not wellexplored and it is uncertain how different dietary components influence its composition.Five experimental diets were fed to Arctic charr (Salvelinus alpinus) to investigate their effects on gutmicrobiota. The fish meal in a reference diet was replaced with either intact or extracted yeast cells ofthe species Saccharomyces cerevisiae, the filamentous fungi Rhizopus oryzae or meal from blue mussel(Mytilus edulis). The microbiota was characterised in samples collected from the proximal and distalintestine using 16S rRNA gene amplicon sequencing with Illumina MiSeq.Sequence data showed that the gut microbiota was dominated by Firmicutes and Proteobacteria, whichrepresented 85% of total community abundance, with lactic acid bacteria representing 36.2%. Principalcomponent analysis (PCA) of the data revealed that the microbiota in proximal and distal regions ofthe intestine had similar composition and that replacement of fish meal with yeast and filamentousfungi affected microbiota composition, primarily with higher relative proportions of Photobacterium andLactobacillus.Lactic acid bacteria were a dominant fraction of the intestinal microbiota in Arctic charr. Microbialbased feeds were associated with similar changes in microbiota composition, but contrasting to the fish-meal based reference diet. Microbiota composition was similar in the proximal and distal gut, but dietaryresponses were specific to gut segment