Comparative Genomic and Functional Characterization of Lactobacillus casei Group (LCG) Probiotic Strains Isolated from Traditional Yogurts by Next-Generation Sequencing

Lactobacillus casei group which is consists of Lactobacillus rhamnosus, Lactobacillus casei, and Lactobacillus paracaseiis an important group of probiotic lactic acid bacteria with numerous commercial and applied health applications. In the present study, we comparatively analysed the genomes of three strains (Lactobacillus rhamnosus ATCC 53103, Lactobacillus casei L9, and Lactobacillus paracasei W56) of LCG isolated from traditional yogurt samples using the next-generation sequencing approach. The GC contents of the characterized strains were in the range of 46.03 to 46.52% while the protein-coding sequences (CDS) were in the range of 2544 to 2888. The pan-genome analysis of the three strains identified a total of 5449 genes with 377 as core genes. The functional characterization by subsystem category distribution analysis revealed "Carbohydrates" is the largest subsystem followed by "protein metabolism" while the biological pathway analysis by the Kyoto encyclopedia of genes and genomes (KEGG) database identified the "metabolic and biosynthesis of secondary metabolites pathway" as the dominant one. Similarly, the functional characterization by eggNOG database revealed that the COGs associated with "Carbohydrate transport and metabolism" were dominant. These find-ings provide a broader understanding of the genome features as well as their functional characterization of the famous probiotic bacterial group.