Genome-Informed Characterization of Lactiplantibacillus plantarum ND88 with Inhibitory Activity against Representative Oral Pathogens

Lactiplantibacillus plantarum ND88, a human-derived strain with putative probiotic-associated traits, was taxonomically confirmed by whole-genome sequencing and comparative genomic analysis. Average nucleotide identity (ANI) analysis showed that ND88 clustered within the L. plantarum species group, sharing > 98% identity with representative reference genomes. Comparative pangenome analysis of ND88 and 20 L. plantarum genomes revealed multiple ND88-specific and enriched orthogroups, indicating strain-level genomic diversification. Genome-informed Pfam domain annotation predicted several adhesion-associated features, including repeated MucBP domains and predicted surface-associated proteins carrying LPxTG motifs and secretion signals. Consistent with this, L. plantarum ND88 exhibited approximately 2.2-fold greater adhesion to intestinal epithelial cells compared with Lactocaseibacillus rhamnosus GG. The strain exhibited strong acid tolerance, maintaining approximately 98% survival at pH 3. Genome mining using BAGEL4 identified a plantaricin bacteriocin biosynthetic locus, providing a genetic basis for antimicrobial activity. Correspondingly, ND88 inhibited representative oral pathogens, reducing adhesion by 29.8–57.4% and growth by 47.7–97.1% in co-culture assays. Genome-based safety assessment indicated the absence of virulence-associated genes and acquired antimicrobial resistance determinants. Although the minimum inhibitory concentrations for gentamicin and kanamycin were above EFSA microbiological cut-off values, no genomic evidence of acquired resistance was detected. ND88 also showed no hemolytic activity, the absence of bile salt hydrolase activity, and low D-lactate production (0.0068 g/L), comparable to GRAS-certified L. plantarum strains. These results demonstrate that ND88 is a genetically safe strain with experimentally supported probiotic-associated traits. Genome-informed comparative genomics confirmed the taxonomic identity of L. plantarum ND88. ND88 showed 98% survival at pH 3 and high epithelial adhesion. ND88 inhibited oral pathogens and reduced their adhesion to epithelial cells. ND88 showed no hemolysis, low D-lactate production, and no acquired antibiotic resistance genes. This study illustrates a genome-informed approach for identifying candidate probiotic strains.