Functional and genomic profiling of lactic acid bacteria reveals specific traits as potential probiotics

The probiotic potential of lactic acid bacteria (LAB) and the subsequent long history of safe use in fermented foods and the human gastrointestinal tract are well-established. However, probiotic properties often vary considerably among species and strains, and the genomic determinants underlying these functional differences remain incompletely understood. Thus, this study obtained 27 LAB isolates from human oral cavity and cheese samples, and characterized these isolates to evaluate the associated probiotic potential using an integrative phenotypic and genomic approach. Molecular identification based on 16S rRNA gene sequencing assigned these isolates to five LAB species: Lactobacillus rhamnosus, Lactobacillus curvatus, Lactobacillus reuteri, Lactococcus lactis, and Lactobacillus paracasei, with L. rhamnosus being the most prevalent. In vitro assays revealed substantial variation among isolates in key probiotic traits, including acid and bile tolerance, adhesion to HT-29 intestinal epithelial cells, antimicrobial activity against pathogenic microorganisms, and antibiotic susceptibility. Notably, L. rhamnosus and L. reuteri exhibited the highest tolerance to acidic conditions and strong antimicrobial activities, while L. reuteri showed the greatest adhesion ability. Based on these phenotypic characteristics, seven representative strains were selected for whole-genome sequencing and comparative genomic analysis. Genomic characterization revealed genome sizes ranging from approximately 2.0-3.0 Mb and conserved functional gene categories related to metabolic processes and catalytic activity. Comparative analysis of adhesion-related genes identified expanded gene families (galE, lgt, ftsW, ypeA, lytG) linked to cell wall modification, lipoprotein maturation, and autolysin activity. Secondary metabolite predictions suggested a potential association between antimicrobial activity and species-level differences in RiPP-like and polyketide synthase clusters, including genes such as mvaS, lagD, LSEI_2163, and LSEI_2386. Overall, this study provides a comprehensive functional and genomic assessment of diverse LAB isolates and highlights specific genetic features associated with probiotic potential. These findings support the rational selection and development of LAB strains for next-generation probiotic applications.