An integrated genomic and phenotypic insight into safety performance and probiotic potential of a novel strain Pediococcus pentosaceus K6 derived from Tibetan kefir
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.
Genomic and phenotypic results supported the potentials of BGI-N8 and BGI-N9 as candidate probiotic strains with distinct complementary strengths in glycolipid regulation, providing a theoretical basis for their synergistic application.
Jia-Yi Ma, Zhihui Ma, Xinyu Yang et al.· Microorganisms· 0 citations
Two human-derived Pediococcus pentosaceus strains, MIANGUAN and MIANGUAN2, were subjected to integrated genomic and phenotypic characterization and supports their further investigation as potential probiotic candidates.
Yulu Chen, Hui-Xin Shi, Hao Zhang et al.· Probiotics and Antimicrobial...· 0 citations
Lactic acid bacteria are widely recognized for their probiotic potential and their ability to inhibit pathogenic microorganisms through the production of antimicrobial compounds and competitive exclusion mechanisms. Staphylococcus aureus is a globally significant human and animal foodborne pathogen and a major cause of foodborne diseases, posing serious public health concerns. This study aimed to develop a probiotic strain capable of suppressing S. aureus. Lacticaseibacillus rhamnosus strain KFOM 0134 was isolated from salted kimchi cabbage; it demonstrated strong tolerance to acidic and high-bile conditions. It did not exhibit any cytotoxic effects, but displayed significant anti-inflammatory activity and enhanced intestinal adhesion capacity. Notably, KFOM 0134 exerted pronounced antimicrobial activity against S. aureus, highlighting its potential as a functional probiotic. Whole-genome sequencing revealed bacteriocin- and cryptic antimicrobial peptide (AMP)-related genetic determinants, but not any virulence- or transferable antibiotic resistance-associated genes, supporting its pathogenic safety. To further contextualize this strain within species-wide diversity, 402 L. rhamnosus genomes were compared, revealing extensive diversity characterized by an open pangenome structure and clade-associated metabolic differentiation. Phylogenetic positioning and lineage-specific functional signatures provided additional insight into the genetic basis of antimicrobial competence. Overall, phenogenomics of L. rhamnosus KFOM 0134 confirmed its well-defined probiotic potential via experimental validation of functional traits, comprehensive genome-based safety assessments, and the identification of bacteriocin- and AMP-associated genes. These findings substantiate its safety and antimicrobial functionality, supporting its applicability in food safety management and functional food development.
Yoon-Soo Gwak, Hui-Yeon Suh, Hyeong-Rak Yoon et al.· Journal of Microbiology and...· 0 citations
The ban on antibiotic growth promoters in livestock production has created an urgent demand for safe and effective probiotic alternatives derived from indigenous animal microbiota. Here, we isolated Enterococcus hirae HI3 from Hu sheep jejunum and confirmed its species assignment via whole-genome sequencing, with ANI analysis showing 98.92% identity to the E. hirae reference genome. HI3 showed moderate acid tolerance, with survival rates of 19.31% (95% CI: 15.83–22.78%) at pH 2 and 18.40% (95% CI: 17.87–18.94%) at pH 3 after 4 h, and maintained > 50% survival in 2% bile salts. It was susceptible to penicillin, ampicillin, erythromycin, and chloramphenicol. No hemolytic activity was observed, and major enterococcal virulence genes (gelE, cyl, esp, hyl) were absent from the HI3 genome. The HI3 genome (3.06 Mb) consists of one circular chromosome and three circular plasmids. Functional annotation identified 229 carbohydrate metabolism genes (including 65 glycoside hydrolases) and 43 probiotic-related genes involved in acid tolerance (atpA–G, nhaC), bile salt tolerance (cbh), stress responses (clp family, groEL, dnaK, cspA, sod2), and adhesion (ltaS, srtA, eno, epsA). Multiple bacteriocin biosynthetic gene clusters (enterolysin A, class II lanthipeptide, etc.) were identified. Plasmid-borne tetracycline resistance genes tet(M) and tet(L) were detected; however, their functional transferability requires experimental validation. No other known transferable resistance determinants were identified in the genomic analysis. These in vitro and genomic findings represent an initial characterization of E. hirae HI3 and support its potential as a ruminant probiotic candidate. However, in vivo studies are required to validate its colonization capacity, safety, and efficacy in the target ruminant species.
