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<p><i>Lactiplantibacillus plantarum</i> 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 <i>L. plantarum</i> species group, sharing &gt; 98% identity with representative reference genomes. Comparative pangenome analysis of ND88 and 20 <i>L. plantarum</i> 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, <i>L. plantarum</i> ND88 exhibited approximately 2.2-fold greater adhesion to intestinal epithelial cells compared with <i>Lactocaseibacillus rhamnosus</i> 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&#xa0;g/L), comparable to GRAS-certified <i>L. plantarum</i> strains. These results demonstrate that ND88 is a genetically safe strain with experimentally supported probiotic-associated traits.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月25日

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  • Hye Kim,
  • Hyun Ha Lee,
  • Sehyeon Song,
  • Md Ariful Haque,
  • Md Abdur Razzak,
  • Min Ji Jang,
  • Krithika Maki,
  • Seockmo Ku

摘要

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.