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Phylogeny is the study of relationships and evolution between collections of things (genes, proteins, organisms or etc.) that are derived from a common ancestor. It is a useful tool for classifying organisms and gives better results than traditional identification methods based on morphological, metabolic and other phenotypic traits. Pediococcus acidilactici TISTR 2309 is one of the lactic acid bacteria (LAB) that was found in traditional Thai fermented sausages and it has the potential to produce bacteriocin against foodborne Gram positive bacteria, including Bacillus cereus and Staphylococcus aureus. Three phylogenetic trees derived from the Maximum Likelihood, Neighbor-Joining and Maximum Pasimony methods, were compared in order to find the relationship of the strains constructed by each method. The results from phylogenetic analysis of 16S rDNA sequences by these 3 methods indicated that P. acidilactici TISTR 2309 is homogenous to P. acidilactici IMAU60189. However when the same sequence of TISTR 2309 was used as input for search tools of NCBI Blast and ENA, the two databases provided different results of identification and different suggested strains. It was also found that the potential in bacteriocin production of the P. acidilactici TISTR 2309 isolate did not reduce over nine years of laboratory subculture.