Probiotic Potential and Acidification Capacity of Pediococcus acidilactici PA-X1 Isolated from Fermented Yak Yogurt: Phenotypic and Genomic Characterization

Lactic acid bacteria combining probiotic properties with acidification capacity and stress tolerance are valuable for food fermentation but remain insufficiently characterized. In this study, a strain of Pediococcus acidilactici, designated PA-X1, was isolated from pastoral fermented yak yogurt collected from the Qinghai–Tibet Plateau. Its in vitro probiotic-related properties, acidification performance, genomic characteristics, and expression patterns of key genes associated with acidification-related metabolism were investigated. After 24 h of fermentation, the broth pH decreased to 3.75 ± 0.02 and the L-lactic acid concentration reached 8.53 ± 0.23 g/L. The glucose concentration decreased from the measured initial value of 20.0 g/L at 0 h to 6.00 g/L at 24 h, corresponding to 70.0% glucose consumption. PA-X1 showed a survival rate of 94.64 ± 0.10% at pH 3.0, and its culture supernatant inhibited all three tested indicator bacteria, namely Escherichia coli, Salmonella enterica, and Staphylococcus aureus, in vitro. Genomic analysis identified multiple genes associated with acidification-related metabolism, including those involved in the phosphotransferase system (PTS), the Embden–Meyerhof–Parnas pathway, pyruvate metabolism and lactate synthesis. Additionally, the PTS-related genes ptsI, ptsH, and crr were significantly upregulated under high-glucose conditions (40 g/L), whereas low-pH conditions induced varying degrees of upregulation of glycolysis- and pyruvate-metabolism-related genes, including pgk, eno, tpiA, ldhA, ldhL, and ackA. Together, these phenotypic, genomic, and gene-expression results suggest that the acidification phenotype of PA-X1 may be associated with carbohydrate uptake, glycolysis, pyruvate metabolism, and organic acid formation. Overall, the combined probiotic-related, acidification, and antibacterial properties of PA-X1 support its potential as a functional starter culture for developing probiotic fermented foods with improved microbial safety and functional value.