Application of Repetitive Extragenic Palindromic El ements Based on PCR in Detection of Genetic Relationship o f Lactic Acid Bacteria Species Isolated from Traditional Fermented Food Products

Abstract

Tarkhineh is one of the traditional foods in Iran and a rich source of probiotic bacteria. The objective of this study was to identi fy the probiotic bacteria isolated from Tarkhineh using 16S rRNA gene sequencing and molecu lar typing with repetitive extragenic palindromic–PCR (REP-PCR). In total, 20 different bacteria were isolated from traditional dairy products and Tarkhineh. Mole cular identification of the isolates was carried out by 16S rRNA gene sequencing, and DN A sequences of isolates deposited in GenBank. The REP-PCR reaction by REP1R-I, REP2-I and REP1R-I+REP2-I markers was performed for fingerprinting and charac terization of the isolates. Un- weighted pair group method with arithmetic mean (UP GMA) clustering methods were performed based on Dice similarity. The REP1R-I pri mer grouped isolates into three, and REP2-I and REP1R-I+REP2-I grouped all isolates into four main clusters in dendrograms. In all analyses, isolates of Lactobacillus casei , Lactobacillus brevis, Lactobacillus plantarum , and Entrococcus facium formed separate clusters. The results of sequencing corresponded to clustering in the dendro gram. According to the results, REP- PCR is an accurate technique for determining the ge netic diversity of lactic acid bacteria species. Keywords : 16S rDNA sequencing, REP-PCR fingerprinting.