Complete Genome Sequence Analysis, Probiotic Properties, and Safety Assessment of Healthy Human-Derived Pediococcus pentosaceus.

The probiotic potential of microorganisms is generally strain-specific and requires comprehensive evaluation at the strain level. In this study, two human-derived Pediococcus pentosaceus strains, MIANGUAN and MIANGUAN2, which have previously demonstrated beneficial effects in animal models, were subjected to integrated genomic and phenotypic characterization. Complete genome sequencing revealed that both strains possessed one chromosome and four plasmids, together with genetic features associated with carbohydrate metabolism, stress adaptation, adhesion-related functions, and biosynthesis of secondary metabolites. Pan-genome analysis further identified strain-specific genetic characteristics and provided insights into their potential ecological adaptation. In vitro assays conducted according to FAO/WHO recommendations demonstrated tolerance to simulated gastrointestinal conditions, aggregation capacity, adhesion ability, and antimicrobial activity. Additional safety assessments showed absence of hemolytic activity, gelatinase activity, cytotoxicity, and transferable antibiotic resistance determinants. A Penocin_A-associated gene cluster was identified in MIANGUAN2; however, neutralized cell-free supernatant assays indicated that organic acids were the major contributors to antibacterial activity under the tested conditions. Collectively, this study provides a comprehensive genomic and experimental characterization of two human-derived P. pentosaceus strains and supports their further investigation as potential probiotic candidates.