Efficiency of the V3 region of 16S rDNA and the rpoB gene for bacterial community detection in Thai traditional fermented shrimp (Kung-Som) using PCR-DGGE techniques

Abstract

Kung-Som is one of several Thai traditional fermented shrimp products, that is especially popular in the southern part of Thailand. This is the first report to reveal the bacterial communities in the finished product of Kung-Som. Ten Kung-Som samples were evaluated using the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) methodology combined with appropriate primers to study the dynamics of the bacterial population. Two primer sets (V3; 341f(GC)- 518r and rpoB; rpoB1698f(GC)-rpoB2014r primers) were considered as a possible tool for the differentiation of bacteria and compared with respect to their efficiency of 16S rDNA and rpoB gene amplification. PCR-DGGE analysis of both the V3-region and rpoB amplicon was successfully applied to discriminate between lactic acid bacteria and Gram positive strains in the bacterial communities of Kung-Som. In conclusion, the application of these two primer sets using PCR-DGGE techniques is a useful tool for analyzing the bacterial diversity in Kung-Som. Moreover, these preliminary results provide useful information for further isolation of desired bacterial strains that could be used as a starter culture in order to improve the quality of Kung-Som.

Keywords

• Kung-Som
• rpoB gene
• V3 region
• PCR-DGGE
• bacterial community