From Fermentation to Function: Genomic Diversity and Probiotic Potential in the Reclassified Lactobacillus Lineage

The genus Lactobacillus has long been recognized for its essential roles in food fermentation and as a key component of probiotic therapy. Recent advancements in taxonomic classification have led to the reorganization of many species into separate genera, opening new avenues for understanding their genetic and functional diversity. In this study, we performed an extensive genomic comparison of 3,813 high-quality genomes from 35 species previously classified under Lactobacillus. Our focus was on identifying functional genes, bacteriocin clusters, secondary metabolite biosynthesis gene clusters (BGCs), and carbohydrate-active enzymes (CAZymes), which are central to the beneficial properties of these bacteria. Among the species analyzed, Lactiplantibacillus plantarum stood out due to its adaptability in carbohydrate metabolism and its ability to perform vital probiotic potential, such as antimicrobial activity, γ-aminobutyric acid (GABA) production, and resilience to environmental stress. We also observed important species-specific variation in functional traits, with Lacticaseibacillus rhamnosus showing high prevalence of antimicrobial genes, while Lactobacillus iners displayed specialized metabolic pathways that enable it to thrive in unique ecological environments. Notably, no classical virulence factors were detected, indicating a generally favorable genomic safety profile, although experimental validation remains necessary prior to probiotic application. This study highlights the remarkable genetic and functional diversity within the reclassified Lactobacillus group, offering valuable insights into their roles in food fermentation, human health, and biotechnological applications. The findings provide a foundation for advancing the development of novel probiotics and functional foods, with potential benefits for human health and sustainable food production.