Composition of bacterial communities in the intestine, skin and spleen of farmed rainbow trout infected with Vibrio anguillarum

Vibrio anguillarum infection in cultured trout, besides its own harmful effects, can also make the fish more susceptible to other infections, both by swamping the host immune system and by creating the skin lesions that serve as a direct gateway for opportunistic bacteria. Samples of tissue were taken from gut, spleen, and mucus from skin lesions of cage-grown rainbow trout suffering from natural Vibrio infections of varying severity. The fish were caught by a net randomly from four neighboring cages. The animals in these cages were from the same full-sibling family batch, the same age, average weight, and were kept with the same stocking density and feeding regime. In addition, a sample of water was taken to document the planktonic bacteria inhabiting the fish farm at the time of study. Total DNA was isolated from these samples and used to produce v3-v4 SSU rRNA amplicons, which were then sequenced on Illumina MiSeq (2x300 bp) and assembled into 97% identity OTUs. Raw sequencing data deposited at NCBI SRA (project ID PRJNA828372, sequencing run IDs SRR18828104 to SRR18828151) and resulted OTU tables deposited here. Table "OTUs" provides data on the composition of bacterial communities in the spleen, skin and intestines of farmed rainbow trout infected with Vibrio anguillarum (SL-heavy infected, IP-moderately infected, AS-asymptomatic).
The "Taxonomy" table contains a decryption of the taxonomy of these unique OTUs. The obtained 16S rRNA gene sequencing dataset allows analyzing bacteria co-colonizing skin and intestine of the infected fishes along with the pathogenic Vibrio anguillarum, as well as generally providing knowledge on the spread of bacteria between various bodily compartments in infected trout.