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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.
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.
Background/Objectives: Certain strains of Lactobacillus acidophilus are widely used as probiotics. However, their functional potential for female reproductive tract health remains insufficiently characterized. While most studies have focused on individual strains, the distribution of putative probiotic-associated genes across the species remains unclear. This study aimed to evaluate the vaginal probiotic potential of Lb. acidophilus using population genomic analysis and comparative phenotypic characterization. Methods: Pan-genomic analysis was performed on 109 Lb. acidophilus genomes (107 public genomes and 2 vaginal isolates). Putative probiotic-associated gene clusters were identified by functional annotation, categorized into functional modules, and compared among ecological-origin groups. Two vaginal isolates (strains A2 and A3) were characterized in vitro for growth under different pH conditions, cell surface hydrophobicity, lactic acid and hydrogen peroxide production, antimicrobial activity, hemolysis, and antimicrobial susceptibility. Results: The Lb. acidophilus pan-genome was closed, with 1782 of 1902 gene clusters (93.69%) classified as core. Thirty-six putative probiotic-associated gene clusters were identified and grouped into four modules: environmental tolerance, adhesion/colonization, exopolysaccharide/biofilm synthesis, and nutrient metabolism/microbial competition. Thirty-four of the 36 gene clusters were present in all 109 genomes, and no general ecological origin-specific distribution pattern was observed. Three bacteriocin-related gene clusters were conserved across all genomes. A2 and A3 exhibited similar lactic acid production and growth patterns at pH 4–6. Both produced relatively low amounts of hydrogen peroxide compared with the reference strains. A3 showed higher cell surface hydrophobicity and moderate inhibition against Gardnerella vaginalis, while A2 showed no inhibition of this organism. Both isolates were non-hemolytic, and were susceptible to vancomycin and linezolid, resistant to clindamycin, and non-susceptible to daptomycin. No acquired antibiotic resistance genes were detected. Conclusions: Most putative probiotic-associated gene clusters were conserved across the Lb. acidophilus population, whereas A2 and A3 showed strain-dependent phenotypic differences. These findings support combining population genomic analysis with strain-level phenotypic testing when selecting Lb. acidophilus candidates for bacterial vaginal infections.
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.
Lactic acid bacteria (LAB) are regarded as promising probiotics with multiple beneficial properties for humans’ and animals’ health. In this study, ten LAB isolates were screened and Lactiplantibacillus plantarum (L. plantarum) CLPX21 was selected as a candidate strain with its probiotic potential based on in vitro screening of antimicrobial activity and environmental stress tolerance, including its resistance to acidic environments and bile salts. This strain displayed adhesion capacity with an auto-aggregation rate of 47.15% at 24 h, co-aggregation rates above 67% with pathogenic bacteria, and an ability to adhere to IPEC-J2 cells (6.37%). CLPX21 showed broad-spectrum antimicrobial activity against common foodborne pathogens including Escherichia coli (E. coli), Salmonella, and Staphylococcus aureus. In addition, CLPX21 inhibited E. coli biofilm formation. Furthermore, CLPX21 significantly suppressed E. coli-induced inflammatory cytokine production in mouse peritoneal macrophages. Importantly, CLPX21 did not exhibit hemolytic activity. Genomic analysis further revealed that the CLPX21 genome encoded multiple functional genes and gene clusters, including biosynthesis of bacteriocins and secondary metabolites associated with antimicrobial and antioxidant functions, which provide a genetic basis for its beneficial phenotypic characteristics. In conclusion, L. plantarum CLPX21 displays probiotic properties with potent antimicrobial and anti-inflammatory activities, representing a promising candidate strain for applications in the food and health industries.
Katak, a traditional Bulgarian fermented dairy product distinguished by its unique sensory characteristics and extended shelf life, represents a valuable source of autochthonous microorganisms whose functional and genomic properties remain insufficiently explored. In the present study, strain L3, isolated from katak, was comprehensively characterized by a polyphasic approach integrating classical microbiological methods, molecular identification, and whole-genome sequencing. Functional assessment revealed a broad spectrum of antimicrobial activity against pathogenic bacteria and food-associated fungi, accompanied by pronounced radical-scavenging and antioxidant capacities. The strain also exhibited high transit tolerance in simulated gut passage and a favorable antibiotic susceptibility profile, indicating its potential as a probiotic candidate. Whole-genome sequencing confirmed the taxonomic affiliation of the isolate as Lactiplantibacillus plantarum and enabled the identification of genetic determinants associated with stress response, environmental adaptation, oxidative stress protection, biofilm formation, and antimicrobial activity. The genomic analysis complemented the in vitro findings by identifying genetic determinants consistent with the observed phenotypic traits, supporting the genetic potential of strain L3 for probiotic-associated functions. The integration of phenotypic and genomic evidence allowed a comprehensive evaluation of L. plantarum L3 and demonstrated that its probiotic-related properties are underpinned by a diverse repertoire of functional genes. These findings identify L3 as a promising candidate for further biotechnological/probiotic assessment.
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