SSU rRNA sequencing data for bacterial communities associated with infected rainbow trout (.

infection in aquacultured trout, besides its own harmful effects, can also make the fish more susceptible to other infections, both by swamping the host's immune system and by creating the skin lesions that serve as a direct gateway for opportunistic bacteria. Tissue samples were taken from the intestines, spleen and skin lesions of cage-grown rainbow trout suffering from natural infections of varying severity. In addition, a water sample was taken to document the planktonic bacteria inhabiting the fish farm at the time of the study. Total DNA was isolated from these samples and used to produce v3-v4 SSU rRNA amplicons, which were then sequenced on Illumina MiSeq (2 × 300 bp) and assembled into 97% identity OTUs. This dataset allows analysis of bacteria co-colonizing the skin and intestines of infected fish along with the pathogenic , as well as provides information on the spread of bacteria between various bodily compartments of trout.