A functional approach to the intestinal microbiome of rainbow trout (Oncorhynchus mykiss) affected by a plant-based diet and handling stress
The present thesis investigated the influence of plant-based feeding and handling stress on the gut microbiome of two rainbow trout genetic lines using 16S rRNA gene analysis. In addition, the functional contributions of bacteria within the gut mucosa were assessed using RNA sequencing. The results demonstrated that the use of a plant-based diet combined with simulated handling stress had no significant effect on classical fish performance parameters in either trout genetic line. However, the results also indicated that handling stress significantly affected the bacterial composition of the gut content of trout genetic line B, whereas in trout genetic line A an interaction of stress and diet induced a shift in the bacterial community. Furthermore, the plant-based diet had a consistent significant effect on the resident microbiota of the intestinal mucosa in both trout genetic lines. While different responses to the treatments were observed in the transient and resident microbiota, an overlap of bacteria from the genera Cetobacterium, Mycoplasma, and Photobacterium was observed in both communities, indicating that they are important taxa in the gut of rainbow trout. Functional activities of the bacteria, revealed that 499 transcripts were significantly regulated by either diet, stress, or their interaction. While none of the regulated transcripts could be annotated by available databases, the metatranscriptome data indicated an up-regulation of cobalamin metabolism and amino acid metabolism with evidence for arginine biosynthesis independent of diet and stress. In conclusion, the gut microbiome of two trout genetic lines was differentially affected by diet type and stress, while classical performance parameters remained unchanged, revealing the microbiome as an early indicator of aquaculture practices.
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