In this study, we conducted interspecific competition experiments between two Atlantic salmon populations and four ecologically similar salmonids. For each Atlantic salmon population, we had six treatments: Atlantic salmon alone, Atlantic salmon reared with one of the four competing species and Atlantic salmon reared with all the four species together. After 10 months of rearing in semi-natural stream tanks, we characterized the gut microbiota for 178 Atlantic salmon using massively parallel sequencing of the 16S rRNA gene.