Divergent Oral Microbiome Outcomes of hydrogen peroxide, Chlorhexidine, and Essential Oil Mouthwashes

Objectives: Oral microbiome control is important for dental operation with open wound. Preoperative mouthwashes are widely used for microbiome reducing. Our study aims to compare the effects of hydrogen peroxide (H2O2), chlorhexidine, and essential oil mouthwashes through microbiome analysis, with the goal of identifying formulations that selectively target and suppress pathogenic bacteria while preserving beneficial commensal species and promoting a balanced oral microbiome.Methods: 12 healthy volunteers were randomly divided into H2O2 group, chlorhexidine group, and essential oil mouthwash group. Saliva was collected at three time points: 5 minutes after rinsing with water, 5 minutes and 1 hour after rinsing with one of the three mouthwashes. Microbiome of these samples were analyzed from the 16S rRNA gene sequence.Results: The alpha diversity and beta diversity showed no significant statistical differences. The oral microbiome composition at the genus level presented slightly change among all time points in H2O2 group and essential oil group, but presented significant change in chlorhexidine group. In H2O2 group, the proportion of Neisseria decreased significantly, while Actinomyces increased. In chlorhexidine group, Porphyromonas, Veillonella, Streptococcus, Neisseria and Gemella decreased significantly. In essential oil mouthwash group, Leptotrichia decreased significantly, Haemophilus increased significantly.Conclusions: Compared to H2O2, essential oil mouthwash and chlorhexidine exhibit stronger bacteriostatic effects against oral pathogens. However, chlorhexidine may disrupt microbial equilibrium, whereas essential oil mouthwash demonstrates superior efficacy in maintaining a balanced oral microbiome. Thus, essential oil mouthwash could serve as a viable alternative to chlorhexidine for oral microbiome management, though long-term efficacy requires further investigation.