The microbiota knows: handling-stress and diet transform the microbial landscape in the gut content of rainbow trout in RAS

Background: The aim of the present study was to characterize the effects of handling stress on the microbiome in the intestinal gut contents of rainbow trout ( Oncorhynchus mykiss ) from two different breeding lines fed with plant-based diets. Two experimental diets were provided for 59 days to all female trout and half of the fish were shooed with a fishing net twice per day to induce long-term stress (groups 0 and 1) in a fully recirculating aquaculture system (RAS). Experimental diets were formulated according to commercial trout diets differing in fish meal (35 % diet F, 7 % diet V) and plant-based proteins (47% diet F, 73% diet V). Results: : No differences in performance parameters were found between treatment groups. By using 16S rRNA amplicon sequencing of the hypervariable region V3/V4 we examined the microbial community in the total gut content of fish at the end of the trial. We discovered no significant differences in alpha diversity induced by one of the two factors within both trout lines. However, the microbial composition is significantly driven by an interaction of stress and diet in trout line A. Otherwise, in trout line B the main factor was stress. The communities of both breeding lines were predominantly colonized with bacteria from the phyla Fusobacteriota, Firmicutes , Proteobacteria , Actinobacteriota and Bacteroidota. The most varying and most abundant taxa have been found to be Firmicutes and Fusobacteriota , where at the genus level Cetobacterium and Mycoplasma are key components in terms of adaptation. Conclusion: We conclude, that microbial gut composition is highly influenced by stress which is presupposed by diet formulation and trout origin but constant microbial diversity and performance parameter.