Determination of bacteria in Corbicula fluminea tissue using 16S rRNA gene sequences

Abstract

Corbicula fluminea is a highly consumed traditional snack by the locals in Kelantan, Malaysia. However, the consumption is suspected to be a cause of diarrhoeal disease that originated from bacterial contamination in C. fluminea tissue. Poor handling and unhygienic processing were hypothesised to contribute largely to the bacterial contamination. Hence, this study aims to compare the bacterial community in C. fluminea tissue at each processing stage to determine the root of contamination source in C. fluminea tissue. Polymerase chain reaction was performed to amplify the hypervariable regions V3–V4 of the 16S rRNA gene from bacterial DNA isolated from C. fluminea tissue. The communities at each processing stage were sequenced on the Illumina Miseq platform and then analysed using the Divisive Amplicon Denoising Algorithm 2 pipeline. The sequencing regions were examined using the Silva v132 reference database. A total of 4 195 108 raw reads were obtained from six bacterial DNA samples of C. fluminea, and the assembled reads were assigned to 888 amplicon sequence variants. Proteobacteria (87.8%), Firmicutes (8%) and Bacteroidetes (3.1%) were the most dominant groups at the phylum level, while Aeromonas (47%), Klebsiella (15.7%) and Enterobacter (10.1%) were predominant at the genus level. The presence of these pathogenic bacteria in the C. fluminea, especially in the smoking and selling stages indicate unhygienic handling by human during preparation and selling stages and this could pose a health risk to consumers.