Genomic safety, bacteriocinogenic potential, and probiotic-associated traits of Enterococcus lactis LBM-M3D isolated from the swine gastrointestinal tract

Abstract

Swine production is vital for global food security; however, its sustainability is threatened by the overuse of antibiotics, which contributes to the emergence and dissemination of multidrug-resistant pathogens. Probiotics and bacteriocin-producing bacteria are promising strategies to support animal health and reduce antibiotic dependence. In this study, Enterococcus lactis LBM-M3D, isolated from the porcine gastrointestinal tract, was evaluated for in vitro antimicrobial activity, tolerance to simulated gastrointestinal conditions, genomic safety features, and bacteriocinogenic potential. The strain inhibited several Gram-positive swine-associated pathogens, including Streptococcus suis, Staphylococcus hyicus, Listeria monocytogenes, and Enterococcus faecalis. In addition, LBM-M3D remained viable under simulated gastrointestinal stress conditions, including exposure to pH 3.0 and 0.5% bile salts. Whole-genome sequencing identified four bacteriocin-like sequences, corresponding to enterolysin A, mundticin ATO6, enterocin SE-K4, and enterocin P. No acquired antimicrobial resistance genes were detected in plasmid-associated regions, whereas resistance- and virulence-associated determinants were exclusively chromosomally encoded. Although E. lactis is not currently included in the EFSA Qualified Presumption of Safety (QPS) list due to limited species-level safety data, our genomic analyses provide strain-level evidence supporting the safety of LBM-M3D. Overall, these findings indicate that LBM-M3D possesses probiotic-associated characteristics and represents a promising candidate for further probiotic development in swine production, pending additional functional validation, with potential applications in sustainable livestock systems.