Delayed shifts in salivary microbiota composition following long-term use of 0.06% chlorhexidine toothpaste.

BACKGROUND: Chlorhexidine is a standard antiseptic in periodontal therapy, yet its long-term impact on the commensal oral microbiota and antimicrobial resistance remains unclear. OBJECTIVE: This study evaluated the ecological effects of 0.06% chlorhexidine toothpaste on the salivary microbiota of healthy individuals, focusing on taxonomic composition, functional shifts, and prevalence of predicted antimicrobial resistance pathways. METHODS: This study was designed as a prospective, single-arm interventional trial to evaluate the temporal dynamics of the oral microbiota. Saliva samples were collected from eleven healthy participants at three specific time points: baseline (following a 4-week run-in period using a reference fluoride toothpaste), intervention (after 12 weeks of using 0.06% chlorhexidine digluconate toothpaste), and washout (after a subsequent 12-week period using the reference fluoride toothpaste). Sequencing targeted the 16S rRNA V3-V4 region. RESULTS: Alpha diversity remained stable throughout the study. However, beta diversity analysis revealed significant shifts in community structure, which were most pronounced between the intervention and washout phases. We identified forty-one differentially abundant metabolic pathways, including a significant downregulation of predicted beta-lactam resistance pathways during the washout period. While chlorhexidine did not increase predicted resistance-related pathways, delayed compositional shifts toward gram-negative taxa were observed at the end of the 12-week washout period. CONCLUSION: These findings suggest that 0.06% chlorhexidine is not ecologically neutral, and dental professionals should carefully consider the appropriateness of chlorhexidine for long-term use.Clinical Trial Registration: ClinicalTrials.gov, NCT07570927.