Oral microbiome profiles by periodontitis stage in a Korean population

Background Periodontitis is a chronic inflammatory disease driven by oral microbial dysbiosis. Although the oral microbiome has been characterized in diverse populations, comprehensive profiling across periodontal disease stages defined by the 2018 AAP/EFP classification remains limited in Korean adults. Methods In this pilot prospective cross-sectional study, oral microbiome profiles were characterized in 74 participants classified into three groups: healthy controls ( n = 24), Stage I–II periodontitis ( n = 12), and Stage III–IV periodontitis ( n = 38). Mouthwash samples were collected and subjected to 16S rRNA gene sequencing of the V3–V4 hypervariable region. Alpha diversity, beta diversity (PERMANOVA with sequential covariate adjustment for age, sex, and smoking), differential abundance (MaAsLin2), and core microbiome analyses were performed. Results Stage III–IV periodontitis was associated with significantly higher Shannon diversity, Simpson diversity, and Pielou’s evenness compared to both healthy and Stage I–II groups, indicating increased evenness rather than species richness. Beta diversity analyses revealed significant community-level separation across groups after adjustment for demographic confounders (all p = 0.001). Differential abundance analysis identified 14 genera significantly associated with disease status. Twelve genera were enriched in Stage III–IV, including established periodontal pathogens Tannerella and Treponema, as well as emerging pathobionts Filifactor and Fretibacterium. Rothia and Kingella were enriched in periodontal health, consistent with their roles in nitrate reduction and maintenance of a health-compatible oral environment. Core microbiome analysis identified 40 universally present genera, with Anaeroglobus detected exclusively in Stage III–IV at 100% prevalence. Conclusion These findings support the polymicrobial synergy and dysbiosis model of periodontitis pathogenesis and provide a foundation for developing microbiome-based diagnostic tools for periodontal disease assessment in Korean populations.