Comparative Genomics-Based Evaluation of Lacticaseibacillus rhamnosus KFOM 0134 as a Probiotic against Staphylococcus...

Lactic acid bacteria are widely recognized for their probiotic potential and their ability to inhibit pathogenic microorganisms through the production of antimicrobial compounds and competitive exclusion mechanisms. Staphylococcus aureus is a globally significant human and animal foodborne pathogen and a major cause of foodborne diseases, posing serious public health concerns. This study aimed to develop a probiotic strain capable of suppressing S. aureus. Lacticaseibacillus rhamnosus strain KFOM 0134 was isolated from salted kimchi cabbage; it demonstrated strong tolerance to acidic and high-bile conditions. It did not exhibit any cytotoxic effects, but displayed significant anti-inflammatory activity and enhanced intestinal adhesion capacity. Notably, KFOM 0134 exerted pronounced antimicrobial activity against S. aureus, highlighting its potential as a functional probiotic. Whole-genome sequencing revealed bacteriocin- and cryptic antimicrobial peptide (AMP)-related genetic determinants, but not any virulence- or transferable antibiotic resistance-associated genes, supporting its pathogenic safety. To further contextualize this strain within species-wide diversity, 402 L. rhamnosus genomes were compared, revealing extensive diversity characterized by an open pangenome structure and clade-associated metabolic differentiation. Phylogenetic positioning and lineage-specific functional signatures provided additional insight into the genetic basis of antimicrobial competence. Overall, phenogenomics of L. rhamnosus KFOM 0134 confirmed its well-defined probiotic potential via experimental validation of functional traits, comprehensive genome-based safety assessments, and the identification of bacteriocin- and AMP-associated genes. These findings substantiate its safety and antimicrobial functionality, supporting its applicability in food safety management and functional food development.