Evaluating nanopore sequencing for microbial community characterization in catfish pond water

The aim of this study was to identify appropriate methods for bacterial community profiling of catfish pond water with nanopore sequencing of the 16S rRNA gene. Two forward primers, two reverse primers, and three different polymerase chain reaction (PCR) cycle protocols were tested on a mock community consisting of aquaculture-relevant bacteria. After identifying the most appropriate methods, the accepted protocol was applied to water samples obtained from three catfish ponds each sampled in May, June, August, and September 2020.