An integrated genomic and phenotypic insight into safety performance and probiotic potential of a novel strain Pediococcus pentosaceus K6 derived from Tibetan kefir
TL;DR
Genetic and phenotypic findings support P. pentosaceus K6 as a highly promising candidate for probiotic and biopreservation applications and identify putative type III polyketide synthase and terpene gene clusters, providing genetic candidates for this antimicrobial phenotype.
Abstract
Pediococcus pentosaceus (P. pentosaceus) is a ubiquitous lactic acid bacterium recognized for enhancing the sensory properties, dietary benefits, and safety of fermented foods. This study isolates and characterizes a Tibetan kefir-derived strain, P. pentosaceus K6, using integrated genomic and phenotypic approaches. Whole-genome sequencing and in vitro assays confirmed a favorable safety profile for K6, showing no hemolytic activity or harmful metabolite production, and lacking pathogenic virulence determinants, transferable antibiotic resistance genes, or functional plasmid conjugation elements. K6 showed strain-specific probiotic features, including 83.83% survival at pH 3.0 for 2 h, 71.16% survival under simulated gastrointestinal digestion, 89.30% auto-aggregation at 48 h, and strong inhibition against Listeria monocytogenes (29.83 ± 0.06 mm). Compared with previously reported P. pentosaceus strains, K6 uniquely combines gastrointestinal tolerance, adhesion-related traits, and anti-Listeria activity. The antiSMASH analysis identified putative type III polyketide synthase and terpene gene clusters, providing genetic candidates for this antimicrobial phenotype. Furthermore, specific carbohydrate-active enzymes and exopolysaccharide biosynthetic genes indicate strong potential for carbohydrate metabolism and food matrix adaptation. Collectively, these genomic and phenotypic findings support P. pentosaceus K6 as a highly promising candidate for probiotic and biopreservation applications.