Identification of bacterial communities related to handling in commercial white-leg shrimp (Litopenaeus vannamei) using metagenomic analysis

Abstract

Post-harvest handling, which includes the use of cold chains and proper hygiene, plays a critical role in maintaining fish quality and food safety. The bacterial community in white-leg shrimp will be affected by differences in the level of hygiene used in traditional and modern markets. This study was aimed to isolate bacterial DNA and identify bacterial communities on the surface of shrimps sold in the commercial market using metagenomic analysis. The research methods covered the isolation of bacterial DNA followed by the metabarcoding analysis of 16S rRNA and bioinformatics analysis. The sequence abundance of bacteria in White-leg shrimp samples were dominated by the genus Myroides, with a relative abundance of 49.18% in traditional markets and 84.89% in modern markets. Bacterial DNA from the skin surface of shrimp from traditional and modern markets has been isolated. The samples of shrimp from traditional markets had a higher relative abundance and diversity of bacteria than samples from modern markets.