Epsilon Open Archive

Abstract

The microbiota has been shown to be important for nutrition and health. It provides the host with an extensive arsenal of dietary enzymes that can contribute to host metabolism by conversion of otherwise undigestible compounds to metabolites that the host can utilize. It can also provide benefits to the host by protecting against colonization of unwanted pathogens and by maintaining mucosal immunity. However, the composition of the microbiota have also been linked with diseases and susceptibility for infections, thus it is evident that the composition of the microbiota has an important role for health. The microbiota in fish is still a fairly unexplored ecosystem and it is not well described how different dietary components influence its composition.

This licentiate thesis focuses on the microbiota in fish and how partial replacement of fishmeal with microbe based protein sources or mussel meal influence the composition and diversity of the gut microbiota, in Arctic charr (Salvelinus alpinus) and rainbow trout (Oncorhynchus mykiss). The gut microbiota was characterized by using 16S rRNA gene amplicon sequencing using Illumina MiSeq. In paper I, five experimental diets were tested; intact (ISC), extracted (ESC) yeast cells of the species Saccharomyces cerevisiae, the micro fungi Rhizobium oryzae (RHO), mussel meal (MYE) and as reference, fishmeal (REF). Analyses showed that the gut microbiota was dominated by Firmicutes and Proteobacteria. Principal component analysis (PCA) of the data revealed that microbiota in proximal and distal regions of the intestine had similar composition. Replacement of fish meal with yeast and filamentous fungi also affected microbiota composition, primarily with higher relative proportions of Photobacterium and Lactobacillus.

In paper II, rainbow trout were fed diets with 3 different inclusion levels of either S. cerevisiae (SC20, SC40, SC60) or Wickerhamomyces anomalus (WA20, WA40, WA60) and as controls, rainbow trout fed fishmeal. Intestinal microbiota were dominated by Leuconostocaceae, Lactobacillaceae and Photobacterium and significant differences in composition of the microbiota were found between fish fed WA40 and WA60 compared with those fed the FM diet. In addition, a reduction in bacterial diversity in fish fed the diet WA40. These results showed that feeding diets with high inclusion of W. anomalus significantly changed the intestinal microbiota of rainbow trout while lower inclusion levels and
diets of S. cerevisiae did not.