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A major challenge in aquaculture is finding nutrient resources that do not compete with human demand and 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 amounts of 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 the intestinal microbiota, that positively affect the intestinal health of fish. The microbiota in fish is not well explored 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 gut microbiota. The fish meal in a reference diet was replaced with either intact or extracted yeast cells of the 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 distal intestine using 16S rRNA gene amplicon sequencing with Illumina MiSeq.Sequence data showed that the gut microbiota was dominated by Firmicutes and Proteobacteria, which represented 85% of total community abundance, with lactic acid bacteria representing 36.2%. Principal component analysis (PCA) of the data revealed that the microbiota in proximal and distal regions of the intestine had similar composition and that replacement of fish meal with yeast and filamentous fungi affected microbiota composition, primarily with higher relative proportions of Photobacterium and Lactobacillus.Lactic acid bacteria were a dominant fraction of the intestinal microbiota in Arctic charr. Microbial based 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 dietary responses were specific to gut segment

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