Comparative functional genomic analysis of table olive-associated Lactiplantibacillus plantarum strains

Table olives are among the most important fermented vegetables in the Mediterranean region, with fermentations largely driven by Lactiplantibacillus species. While Lactiplantibacillus pentosus has been extensively studied at the genomic level, genomic information on olive-associated Lactiplantibacillus plantarum remains scarce. To expand current knowledge, three novel L. plantarum strains isolated from table olive fermentations in Spain (Lpl15 and LPT703) and Greece (B282) were subjected to whole-genome sequencing and comparative genomic analysis. Genome assemblies ranged from 3.25 to 3.50 Mb and contained 3,060–3,328 predicted protein-coding genes. While Illumina assemblies remained fragmented, hybrid sequencing produced a complete genome assembly for strain L. plantarum Lpl15, including a complete chromosome and three plasmids. Comparative analyses incorporating L. plantarum genomes from diverse ecological origins, including vegetable fermentations, animal-derived foods, and human-associated environments, were performed using Average Nucleotide Identity (ANI), pangenome analysis, and core-genome phylogeny. Neither ANI nor phylogenomic analyses supported the existence of a distinct lineage associated with table olive fermentations. Functional and metabolic comparisons revealed two major genomic groups linked to ecological origin. Genomes predominantly associated with vegetable fermentations lacked complete nitrogen metabolism pathways, whereas strains of animal origin generally retained these functions. In addition, vegetable-associated strains showed an enrichment of genes involved in exopolysaccharide biosynthesis. Analyses of protein families, domains, and mobilome-related elements further revealed niche-associated genomic patterns. Overall, these results indicate that L. plantarum from table olive fermentations does not constitute a distinct evolutionary lineage. Instead, adaptation appears to be reflected in functional and accessory genomic traits associated with ecological origin, providing new insights into the diversity and adaptive potential of this species across different environments.