Shotgun Metagenomic Analysis Reveals Taxonomic and Functional Transitions in the Salivary Microbiome During Periodontal Disease Progression

Abstract

ABSTRACT Aim To characterise multi‐kingdom salivary microbiome profiles across clinically defined periodontal states and identify stage‐specific taxonomic and functional alterations using shotgun metagenomic sequencing. Materials and Methods In this cross‐sectional study, 204 adults (mean age 40.3 ± 7.6 years) from the SECRETO study (NCT01934725) underwent clinical and radiographic oral examinations and were classified into six periodontal groups: periodontal health, localised gingivitis, generalised gingivitis, gingivitis with pockets, mild periodontitis (Stages I–II) and severe periodontitis (Stages III–IV). Saliva samples were analysed using shotgun metagenomic sequencing to evaluate microbial diversity, taxonomic composition and functional pathways. Results Beta diversity differed between periodontal health and the different disease states (Bray–Curtis: p = 0.049; Jaccard: p = 0.043). Gingivitis with pockets and severe periodontitis showed a significant enrichment of disease‐associated species Porphyromonas gingivalis , Tannerella forsythia , Treponema denticola , Porphyromonas endodontalis , Fusobacterium nucleatum and Parvimonas micra . Among non‐bacterial taxa, Candida , Moineauvirus , Pyricularia and Roseolovirus were the predominant genera. A composite metagenomic classifier showed high discriminative performance for gingivitis with pockets (AUC = 0.90; 95% CI: 0.770–1.000) and severe periodontitis (AUC = 0.865; 95% CI: 0.762–0.968). Conclusion Salivary multi‐kingdom microbiome transitions closely reflect the progression of periodontal disease and provide promising biomarkers for identifying at‐risk individuals.