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

Tarkhineh is one of the traditional foods in Iran and a rich source of probiotic bacteria. The objective of this study was to identify the probiotic bacteria isolated from Tarkhineh using ۱۶S rRNA gene sequencing and molecular typing with repetitive extragenic palindromic–PCR (REP-PCR). In total, ۲۰ different bacteria were isolated from traditional dairy products and Tarkhineh. Molecular identification of the isolates was carried out by ۱۶S rRNA gene sequencing, and DNA sequences of isolates deposited in GenBank. The REP-PCR reaction by REP۱R-I, REP۲-I and REP۱R-I+REP۲-I markers was performed for fingerprinting and characterization of the isolates. Un-weighted pair group method with arithmetic mean (UPGMA) clustering methods were performed based on Dice similarity. The REP۱R-I primer grouped isolates into three, and REP۲-I and REP۱R-I+REP۲-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 dendrogram. According to the results, REP-PCR is an accurate technique for determining the genetic diversity of lactic acid bacteria species.