Investigation on the rainbow-trout (Oncorhynchus mykiss) fillets resistome and bacterial communities

This study aims at characterizing the bacterial communities of the rainbow-trout fillets. Rainbow-trout were sampled from two farms (code = A or B) On each farm, 28 fish were sampled (coded 01 to 28), of which fourteen were processed in the laboratory (code = R) and fourteen were processed in a processing factory (code = F). Overall, 56 samples were analysed (14 samples for each condition). The bacterial communities of the samples were analysed using Illumina MiSeq amplicon sequencing targeting the V3-V4 fragment of the 16S rRNA gene, averaging a sequencing depth of ~6000 reads/sample.