Given the increasing significance of aquaculture in animal protein production, several researchers started to investigate the gut microbiota of several aquatic organisms. In this context, our study aimed to characterize the core intestinal microbiota of the brook trout (Salvelinus fontinalis ), a fish species that can be found both in farmed and natural environments in Italy, where it is considered an invasive species.
This salmonid species is of economic and environmental importance to several countries, including Italy. In this research, we conducted an analysis of the microbiota present in farmed and wild S. fontinalis with a specific focus on distinguishing between the intestinal wall and the contents of the middle section of the intestine.
A total of 66 individuals, all aged 2+ years, were included in the study, comprising 46 wild individuals and 20 farmed brook trout from two different years. We employed a 16S metabarcoding approach, targeting the V3–V4 hypervariable regions of the 16S rRNA, to obtain microbiota data. Our findings revealed that the core microbiota in these fish species mainly consisted of Proteobacteria (both Alpha - and Gammaproteobacteria ), Actinobacteria, Firmicutes (comprising Bacilli and Clostridia ), and Fusobacteria exclusively in farmed specimens. The presence of Fusobacteria in farmed individuals is likely linked to their fishmeal-based diet.
Furthermore, our analysis of alpha and beta diversity demonstrated discernible differences between wild and farmed fish. Notably, we identified statistically significant differences in microbiota composition between the intestinal walls and contents of wild fish, whereas no variations were observed in the farmed fish.
This study represents the first examination of intestinal microbiota in S. fontinalis, encompassing both farmed and wild individuals. Future research endeavours may explore the comparative aspects of our data with those pertaining to other fish species, as well as delve into the analysis of different portions of the brook trout intestine
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