Effects of chlorhexidine and a polyherbal mouthwash on the oral microbiome and user satisfaction: a randomized controlled trial

Abstract

Objective

This study aimed to comparatively evaluate the effects of polyherbal, chlorhexidine (CHX), and normal saline (NCC) mouthwashes on oral microbiome composition, microbial metabolic pathways, and patient-reported outcomes, with the goal of assessing the potential of polyherbal mouthwash as a natural alternative to CHX for managing gingivitis, while aiming to minimize CHX-associated microbial dysbiosis.

Methods

A randomized, double-blind trial was conducted among 27 patients with gingivitis, randomly assigned to polyherbal, CHX, or NCC mouthwash groups. Participants used the assigned mouthwash twice daily for 7 days. Saliva samples were analyzed via 16 S rRNA sequencing to assess microbial diversity (alpha and beta) and taxonomic composition. Differential taxa and pathways were identified using FDR-corrected Wilcoxon tests and log₂ fold-change analysis. Patient-reported outcomes were evaluated using numerical rating scales (NRS).

Results

The polyherbal mouthwash demonstrated significantly higher patient acceptability than CHX and NCC, with superior scores in taste, smell, texture, moisture retention, overall satisfaction, and willingness for continued use (p < 0.05). While CHX exhibited strong antimicrobial activity, its alcohol-containing formulation markedly disrupted microbial diversity, increased potentially dysbiotic genera (Streptococcus, Porphyromonas), and altered 23 metabolic pathways associated with dysbiosis. In contrast, the polyherbal mouthwash—which also contained cetylpyridinium chloride (CPC)— selectively increased beneficial genera (Amnipila, Absconditabacteriales [SR1], Peptostreptococcus), preserved overall microbial diversity, and modulated only two pathways, notably upregulating L-isoleucine biosynthesis.

Conclusion

The polyherbal mouthwash represents a promising alternative to CHX, demonstrating selective microbial modulation, preservation of microbiome stability, and enhanced patient acceptability. These findings support its potential integration into routine oral healthcare as a microbiome-friendly and patient-acceptable solution. Further studies are warranted to evaluate CPC-free polyherbal formulations across larger and more diverse populations over extended durations.