Genomic insights into Lacticaseibacillus chiayiensis PD2 isolated from Southern Thai fermented fish and its potential for probiotic and antibacterial activity against foodborne pathogens

Traditional fermented foods are rich sources of beneficial microorganisms, particularly lactic acid bacteria (LAB), which contribute to food preservation and host health. In this study, Lacticaseibacillus chiayiensis PD2, isolated from a Thai fermented fish product, was genomically and functionally characterized to evaluate its probiotic potential. The whole-genome sequencing (WGS) revealed a 2.72 Mb genome with two plasmids, harboring genes associated with carbohydrate metabolism, stress adaptation, and environmental fitness. Functional annotation indicated a strong enrichment of genes involved in carbohydrate metabolism, protein and amino acid pathways, and genetic information processing, with 202 strain-specific genes suggesting niche-specific functionality. Key probiotic genes identified include those for acid and bile tolerance (e.g., dltA, dltB ), heat shock response ( clpC, dnaK, dnaJ ), adhesion and biofilm formation ( murA, brpA, luxS ), vitamin biosynthesis, and antioxidant defense ( trxB ). Moreover, biosynthetic gene clusters encoding bacteriocins and RiPP-like peptides were identified. In vitro experiments confirmed that PD2 exhibited strong acid tolerance at pH 3, maintaining nearly 100 % viability during incubation, and high bile salt tolerance at 0.1–0.3 %, with survival rates exceeding 95 %. In addition, PD2 demonstrated notable auto- and co-aggregation abilities with foodborne pathogens including Bacillus cereus , Escherichia coli , Enterococcus faecalis , Listeria monocytogenes , Salmonella Typhi, Vibrio cholerae , and V. parahaemolyticus , along with significant antioxidant activity and broad-spectrum antibacterial effects against those pathogens. Comparative genomic and CAZyme analyses revealed strain-specific adaptations and enzymatic diversity, including the unique presence of polysaccharide lyases, suggesting enhanced metabolic flexibility. Importantly, no virulence or transferable antibiotic resistance genes were detected, supporting its safety. These findings establish L. chiayiensis PD2 as a safe and functional probiotic candidate with promising applications in gut health, functional foods, and natural food preservation. • L. chiayiensis PD2 was isolated from Thai fermented fish and genome analyzed. • The genome encodes plasmid-borne genes for stress and bacteriocin production. •PD2 tolerates acid/bile, aggregates pathogens, and shows antioxidant activity. •Displays antibacterial activity against several foodborne pathogens. No virulence or resistance genes, supporting its probiotic application.