Whole-Genome Analysis and Probiotic Assessment of Pediococcus acidilactici PA_ZFRA1 Isolated from Bovine Rumen

Probiotics identification requires comprehensive safety assessment and probiotic property evaluation. In this study, a Pediococcus acidilactici PA_ZFRA1 strain isolated from the bovine rumen was first characterized by whole-genome sequencing and probiotic properties. The ZFRA1 genome is 2,061,765 bp in length, with 1982 predicted coding sequences and an average GC content of 42.26%. For safety assessment: ZFRA1 shows no hemolytic activity, lacks decarboxylase genes related to biogenic amine synthesis, and poses negligible risk of horizontal transfer for antibiotic resistance genes and virulence factor genes. Regarding probiotic properties, the stress resistance assays demonstrated that ZFRA1 can withstand acid (pH 2, 3, and 4), simulated gastrointestinal fluids, and bile salts (0.3% and 1%). Furthermore, ZFRA1 displayed a considerable antioxidant capacity (75.60% DPPH, 77.35% ABTS free radical scavenging rates, and 1.56 mM TEAC total antioxidant capacity), moderate hydrophobicity (10.42%-20.83%), an auto-aggregation rate of 70.79% at 24 h, an adhesion rate to Caco-2 cells of 11.06%, and high co-aggregation ability (76.50%-83.66%). Moreover, ZFRA1 exhibited inhibitory ability against seven pathogens (E. coli CICC 10372, S. aureus ATCC 27217, C. perfringens ATCC 13124, B. cereus CICC 21290, P. aeruginosa ATCC 10145, S. typhimurium ATCC 14028, and L. monocytogenes ATCC 19111). In summary, the results of genomic analysis combined with in vitro assays showed that ZFRA1 is a promising candidate probiotic strain. However, further in vivo studies are required to validate its safety and efficacy before it can be considered for food fermentation, human consumption, or animal nutrition applications.