Integrated Genomics and Phenotypic Analysis of Pediococcus pentosaceus BGI-N8 and Pediococcus acidilactici BGI-N9: Partial Evidence Suggesting In Vitro Probiotic Properties to Glycolipid Metabolism Regulation Potential

Abstract

Dietary interventions using probiotics actively regulate metabolism in obesity and type 2 diabetes. This study aimed to characterize two novel co-isolated strains, P. pentosaceus BGI-N8 and P. acidilactici BGI-N9, using an integrated genome–phenotype approach. Whole-genome sequencing established their preliminary safety and functional genotypes, followed by in vitro assays measuring gastrointestinal tolerance, adhesion, and metabolic enzyme activity. Genomic analysis revealed that both strains achieved genome-based safety levels, and no high-confidence transferable AMR determinants and canonical virulence factors were identified. Functional annotation showed that BGI-N8 and BGI-N9 contain essential genes for gastrointestinal adaptation, including F0F1-ATPase, the dltA-D operon, and the opp transport system. Phenotypically, BGI-N9 exhibited superior acid resistance (79.3% survival at pH 2.0), while both strains showed robust auto-aggregation (>70%) and high adhesion to HT-29 cells (ranged from 5.4 to 5.9 adherent bacteria per cell). Furthermore, the strains displayed inhibitory activity against selected indicator pathogens (88.6–97.6% inhibition). Notably, BGI-N8 and BGI-N9 showed comparable α-glucosidase inhibitory activities, with inhibition rates of 44.53% and 39.94%, respectively, Both strains also exhibited comparable cholesterol-removal capacities under the tested conditions, with removal rates of 68.76% and 74.49%. Overall, these 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. Further mechanistic, safety, and in vivo studies are required to validate their metabolic-health-related relevance.