Oral microbiome profile before and after nonsurgical periodontal therapy in Stage III periodontitis

Objectives: This study aimed to evaluate the changes in the oral microbiome in patients with Stage III periodontitis before and after non-surgical periodontal therapy using shotgun metagenomic sequencing and advanced bioinformatic analysis. Methods: Subgingival plaque samples were collected from patients diagnosed with Stage III periodontitis at baseline and 4 weeks following non-surgical periodontal therapy. Microbial DNA was extracted and subjected to shotgun metagenomic sequencing. Comprehensive bioinformatic pipelines were employed for taxonomic profiling and functional gene analysis, enabling detailed characterization of microbial composition and shifts over time. Results: Non-surgical periodontal therapy resulted in a significant reduction in key periodontopathic microorganisms. Shotgun metagenomic sequencing facilitated the detection of low-abundance and previously unculturable microbial species, including several novel taxa. Post-therapy samples demonstrated a shift toward a more balanced microbial community, with decreased pathogenic anaerobes and relative enrichment of commensal species. Conclusions: Shotgun metagenomics provides superior taxonomic resolution and functional insights compared to conventional 16S rRNA sequencing. The observed microbial shifts following non-surgical periodontal therapy support the ecological plaque hypothesis and highlight the potential of metagenomic approaches in identifying biomarkers and monitoring disease progression. This approach offers promising applications in personalized periodontal diagnostics and treatment strategies.