The gut microbiota has become a topic of increasing importance in various fields, including aquaculture. Several fish species have been the subject of investigations concerning the intestinal microbiota, comparing different variables including the intestine portions, the environment and diet. In this study, the microbiota of farmed and wild brook trout (Salvelinus fontinalis) was analysed, considering separately wall and content of the medial portion of the intestine. A total of 66 fish (age class 2+) were sampled, of which 46 wild and 20 farmed brook trout, along two different years. Microbiota data were obtained using a 16S metabarcoding approach by analysing the V3-V4 hypervariable regions of the 16S rRNA. Data showed that the core microbiota of these species is represented by Proteobacteria (Alpha- and Gammaproteobacteria), Actinobacteria, Firmicutes (Bacilli and Clostridia) and, only for farmed animals, Fusobacteria. The latter taxon is likely related to the fishmeal-based diet administered to farmed brook trout. Indeed, alpha and beta diversity analysis showed differences between wild and farmed fish. Finally, statistically significant differences in the microbiota composition were observed between intestinal wall and content in wild fish, while no differences were detected in reared animals.
