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.