SSU rRNA metabarcode of bacteria in trout cultured in Angara river
Description
Composition of bacterial communities associated with cultured trout sampled from a fish farm on Angara river. A chronic bacterial disease of unknown etiology was observed on this fish farm; to identify the pathogen for further studies, visibly diseased and apparently healthy fishes were taken into analysis. The primary goal of this analysis was to identify the pathogen, which turned out to be Flavobacterium psychrophilum. Although the community in diseased fishes is heavily dominated by this bacterium, other bacteria inhabiting trout were also detected.
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Total DNA was extracted from 50 mg of anal sphincter tissue with DiaGene anal sphincter DNA extraction kit, amplified using a mixture of primers specific to V3-V4 hypervariable region of SSU rRNA gene and Evrogen KTN-mix PCR kit, and sequenced on Illumina MiSeq with MiSeq v2 Reagent Kit. OTUs were generated at 97% identity threshold using a pipeline based on QIIME 1.9.1. Taxonomic classification was performed using SILVA v132 reference database.