Comparative Genomics Reveals Conserved Bacteriocin-Associated Loci in Lacticaseibacillus paracasei Strains with Anti-MRSA Activity Isolated from Palmyra Palm Sugar

Background: Palmyra palm sugar harbors lactic acid bacteria (LAB) with antimicrobial and probiotic properties. Lacticaseibacillus paracasei strains WU0904 and WU2302 inhibit methicillin-resistant Staphylococcus aureus (MRSA) and reduce biofilm formation. In this study, we aimed to characterize the distribution and architecture of bacteriocin-associated loci across L. paracasei. Methods: A screening set of 67 genomes was filtered at ≥95% average nucleotide identity (ANI) and dereplicated at ≥99.9% ANI, yielding 44 nonredundant L. paracasei genomes. Results: Pangenome analysis identified 7213 gene clusters, comprising 1848 core, 230 soft core, 1528 shell, and 3607 cloud clusters. AntiSMASH analysis identified two major bacteriocin-associated regions in each WU strain. The larger region contained a conserved multipeptide bacteriocin-associated locus comprising predicted prebacteriocins, class II bacteriocins, and genes associated with immunity, regulatory, processing, and export, whereas the smaller region contained a two-gene Blp-family locus. The nine-component backbone of the large locus was complete in 34/44 genomes (77.3%), whereas the small Blp-family locus was present in 18/44 genomes (40.9%). The 59-aa accessory candidate, group_2723, was restricted to WU2302, DmW_181, and CBA7104 and was identical in sequence and syntenic position across these genomes. Phylogenetic analyses showed significant clustering of the small Blp-family locus and group_2723, whereas the large-locus backbone was more broadly distributed. Structural prediction indicated predominantly α-helical conformations among the prioritized bacteriocin candidates. Conclusions: The study findings reveal a shared bacteriocin-associated biosynthetic architecture comprising a conserved backbone and lineage-restricted components, providing specific candidates for future functional validation.