Comparative genomics and functional traits of Weissella cibaria and Weissella confusa isolated from kimchi

Weissella is a fascinating genus that has garnered increasing attention for its probiotic potential and industrial versatility. In this study, we present a detailed genomic and phenotypic investigation of six Weissella strains isolated from kimchi, identified as W. cibaria (254, 256, 258, 260) and W. confusa (255, 257). Genomic analysis revealed species-specific differences, with W. cibaria linked to cell cycle regulation and replication, while W. confusa displayed adaptations for motility and metabolic diversity. Antibiotic resistance gene analysis revealed the presence of daunorubicin resistance (drrA), multidrug resistance determinants (bmr3, lmrA, ykkCD), and species-specific resistance to bicyclomycin (bcr1, bcr2) and quaternary ammonium compounds (qacC). Phenotypic antibiotic susceptibility testing demonstrated intrinsic resistance to vancomycin alongside high sensitivity to ampicillin, erythromycin, chloramphenicol, and gentamicin. Probiotic assessments highlighted significant tolerance to acid, bile salts, and enzymatic stress, with W. cibaria 256 and W. confusa 255 showing superior survivability under simulated gastrointestinal conditions. High surface hydrophobicity observed in W. confusa 255 and 257 further underscores their adhesion capabilities, which are crucial for gut colonization. Exopolysaccharide (EPS) production was further characterized by FTIR analysis, revealing diverse functional groups associated with structural protection and probiotic functionality. Morphological characteristics as determined by field emission scanning electron microscopy (FE-SEM) revealed rod-shaped cells of 1.39-1.87 μm in length and 0.50-0.70 μm in width for W. cibaria strains versus 1.02-1.45 μm in length and 0.54-0.62 μm in width for W. confusa strains. These findings provide novel insights into the genomic and phenotypic underpinnings of Weissella species' probiotic properties, resistance mechanisms, and adaptability to fermented food environments, highlighting their promising applications in functional food development and human health enhancement.