Genomic diversity, functional differentiation and prophage dynamics in Lactiplantibacillus paraplantarum

Lactiplantibacillus (L.) paraplantarum is widely distributed in fermented foods and the gastrointestinal tract of mammals. However, its genomic diversity, evolutionary relationships, functional potential, and ecological adaptation strategies remain poorly understood. In this study, 42 genomes isolated in this study (n = 20) + retrieved from NCBI (n = 22) were analyzed to characterize species-level genomic structure, metabolic versatility, and prophage diversity. Pan-genome analysis revealed an open pan-genome with extensive accessory gene content. Phylogenomic and Average Nucleotide Identity (ANI) analyses showed that strains clustered by clade rather than by isolation habitat. KEGG and CAZy databases indicated enrichment in carbohydrate metabolism and core glycoside hydrolase families, consistent with a fermentative lifestyle, with distinct clade-associated functional signatures. Prophage ANI analysis demonstrated lineage-structured phage diversity closely aligned with host phylogeny. Prophage-associated functional genes also exhibited clade-specific distribution patterns. Phenotypic validation of selected strains exhibited pronounced condition-dependent phenotypic variation, with carbohydrate source, environmental pH, and simulated gastrointestinal stress significantly influencing acid production, growth performance, and survival in a strain-specific manner. This study provides a genomic and phenotypic framework for understanding clade-associated diversification in L. paraplantarum and supports its application in fermentation and probiotic development.