Whole-genome sequencing and in vitro probiotic characterization of Pediococcus pentosaceus ELAB 60WB isolated from fermented cherry tomatoes

Pediococcus pentosaceus is known for its probiotic properties and is used in food fermentation. In this study, we performed in vitro probiotic characterization, genomic analysis, and safety analysis of the P. pentosaceus ELAB 60WB strain isolated from fermented cherry tomatoes. The strain exhibited antagonistic activity, survived exposure to gastric juice, and showed antibiotic activity in vitro. ELAB 60WB adhered to the safety criteria by lacking genes associated with hemolysis and mucin degradation, which may be concerning when administered as a dietary supplement. Whole-genome sequencing revealed a genome size of 1,914,577 bp with a GC content of 37.1%. Phylogenetic analyses revealed close relationships among similar strains. Functional annotation identified 1997 genes, including protein-coding sequences, tRNAs, rRNAs, and tmRNAs, covering 232 SEED subsystems. Within the genome, two bacteriocin genes, penocin A and enterolysin A had the potential to combat the tested pathogens. Manual prediction effectively revealed the presence of probiotic and antibiotic resistance genes in different environments. Carbohydrate metabolism analysis revealed 160 genes in the carbohydrate-active enzymes gene family. Safety assessment revealed no antimicrobial resistance or virulence genes; however, a plasmid, repUS64, was identified, which is common in Lactobacilli. Overall, P. pentosaceus ELAB 60WB contains carbohydrate metabolism genes and probiotic properties that can lead to its potential use in the food industry and in the treatment of metabolic syndrome.