TOWARDS UNDERSTANDING IN MOLECULAR TAXONOMY USING AN In Silico APPROACH: A CASE STUDY IN LACTIC ACID BACTERIA
Keywords:
in silico, molecular taxonomy, lactic acid bacteriaAbstract
In this paper, we propose an in silico analysis using the lactic acid bacteria (LAB) to gain understandingin their diversity, detection, identification and classification. Initially, the 16S rRNA genesequences of 90 LAB species retrieved from the GenBank database were analysed in terms of theirsimilarity and variation using the ClustalW software. The phylogenetic tree was then constructed inorder to investigate their evolutionary relationship. It was found that, according to the tree, theLAB could be grouped into 6 distinct clades similar to the genus classification except the genusLactobacillus. In addition, these results obtained were in agreement with the data derived fromtraditional identification. The probes were also identified based on the multiple sequence alignmentresults to identify the LAB at different levels such as group, genus and species. Furthermore, thein silico PCR-RFLP was performed to reveal their taxonomic classification. Various kinds ofrestriction endonucleases were selected and used to restrict the LAB 16S rRNA genes to observe theirrestriction profiles. It was found that BsaWI, BstDSI and DsaI produced distinct restriction patternssuitable for genus and species determination.
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