For preliminary molecular typing, PCR-based fingerprinting using random amplified polymorphic DNA (RAPD) is the method of choice. In this study, 14 bacterial strains were isolated from different Korean food sources, identified using 16S rRNA gene sequencing, and characterized through RAPD-PCR. Two PCR primers (239 and KAY3) generated a total of 130 RAPD bands, 14 distinct PCR profiles, 10 polymorphic bands, one monomorphic band, and four unique bands. Dendrogram-based analysis with primer 239 showed that all 14 strains could be divided into seven clades out of which clade VII had the maximum of seven. In contrast, dendrogram analysis with the primer KAY3 divided the 14 L. citreum strains into four clades out of which clade IV consisted of a maximum of 10 strains out of 14. This research identified and characterized bacterial populations associated with different Korean foods. The proposed RAPD-PCR method, based on sequence amplification, could easily identify and discriminate the lactic acid bacteria species at the strain-specific level and could be used as a highly reliable genomic fingerprinting tool.

For preliminary molecular typing, PCR-based fingerprinting using random amplified polymorphic DNA (RAPD) is the method of choice. In this study, 14 bacterial strains were isolated from different Korean food sources, identified using 16S rRNA gene sequencing, and characterized through RAPD-PCR. Two PCR primers (239 and KAY3) generated a total of 130 RAPD bands, 14 distinct PCR profiles, 10 polymorphic bands, one monomorphic band, and four unique bands. Dendrogram-based analysis with primer 239 showed that all 14 strains could be divided into seven clades out of which clade VII had the maximum of seven. In contrast, dendrogram analysis with the primer KAY3 divided the 14 L. citreum strains into four clades out of which clade IV consisted of a maximum of 10 strains out of 14. This research identified and characterized bacterial populations associated with different Korean foods. The proposed RAPD-PCR method, based on sequence amplification, could easily identify and discriminate the lactic acid bacteria species at the strain-specific level and could be used as a highly reliable genomic fingerprinting tool.

Fermented food consists of a variety of lactic acid bacteria (LAB) that are also used in the industry as starter cultures. This genus comprises of different species that find importance as a preservatives in food like meat and sausages. Likewise, Lactobacillus brevis has been recognized as GRAS and is a potential probiotic strain extensively being used on an industrial scale. Since such bacteria are directly related to human health, there has been a need to identify and characterize them on the molecular level. In this study, LAB was identified and characterized from various fermented food samples available in South Korea. Two types to PCR-based molecular typing methods were used to analyze the 13 Lactobacillus brevis isolates, of which one was based on difference in the banding patterns originated on agarose gel and the other was related to the sequence analyses of various housekeeping genes in the particular strain. The former rep-PCR technique used three primers namely, REP, ERIC and (GTG)5 that amplified repetitive sequences in the genome and provided characteristic fingerprint profile for each isolate. This clustered the strains in 3 groups with the help of UPGMA method of clustering distinguishing between closely related strains. However, the latter multilocus sequencing typing (MLST) technique provided definite identification of the strains. A set of 7 housekeeping genes were determined as groEL, gyrB, rpoA, rpoB, pheS, recA and dnaK. These genes were amplified and sequenced and were subjected to comparative analysis. Discrete allelic profiles and 13 sequence types (STs) were resolved and minimum spanning tree (MST) was constructed, revealing the genetic relatedness among the isolates. On comparing the results from both the techniques, MLST proved to generate accurate and precise fingerprints owing to the sequence analysis of conserved genes thus providing a scope for research in the monitoring related species.