Probiogenomic and pangenome characterization of Latilactobacillus sakei subsp. sakei from cabbage kimchi: Insights into probiotic potential and safety attributes

초록

A comprehensive probiogenomic analysis of the cabbage kimchi-derived Latilactobacillus sakei subsp. sakei (TAB) strain was performed to determine its functional, safety, and adaptive features. The genome comprised 2 contigs, 2,035,374 bp, 41.13% GC, and 1972 putative coding sequences. A 5326 bp contig was not associated with a plasmid. Phylogenetic analysis showed its close kinship with subsp. sakei strains from different sources. Genome annotation found no virulence, antibiotic resistance, human pathogenicity, or biogenic amine genes. The strain was sensitive to antibiotics below the cutoff range, according to the EFSA, and showed no hemolytic activity. Functional annotation revealed genes for carbohydrate metabolism; oxidative, bile, and acid tolerance; osmotic, heat, and cold stress; and adhesion, suggesting putative probiotic and technological potential. Three biosynthetic gene clusters, RRE region 1, terpene precursor region 2, and T3PKS, were identified in the genome. Thirteen predicted genomic islands (GIs) lacked virulence, antimicrobial resistance, and pathogenicity genes, whereas GI2 had a type IV secretion system integrative and conjugative element but no antibiotic, heavy metal, or virulence genes. Strain-specific genomic flexibility was shown by one intact and one incomplete prophage region. BlastKOALA identified 22 Kyoto Encyclopedia of Genes and Genomics modules, and carbohydrate-active enzyme annotation showed TAB's ability to metabolize galactose in plant-based fermentation environments. A pangenome study found 131 unique gene clusters in the TAB genome compared to subsp. sakei reference genomes, with 25 genes predominantly projected to function in metabolism, cellular activities, signaling, and information storage and processing. Future research warrants cell- and animal-based studies for functional attributes.

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