Development of oral dysbiosis following use of antimicrobial mouthwashes: a systematic review

The oral microbiome maintains the oral and systemic health. The extensive use of antimicrobial mouthwashes to control biofilm-related diseases has increased the concerns about their effect on microbial ecology. Specific formulations may cause microbial shifts which influences both the oral and systemic physiology in an individual. This systematic review evaluates the oral dysbiosis development after antimicrobial mouthwash use and correlates the microbial changes with clinical and systemic outcomes. A comprehensive search in various databases like PubMed, Scopus, etc. (till March 2025) was done. It identified 14 relevant studies from a total of 681 screened records. Risk of bias was assessed using ROB2, ROBINS-I, CRIS, and NOS tools, with data extracted on microbial diversity, taxonomic changes, nitrate reduction capacity, and antibiotic resistance. The findings showed that chlorhexidine caused the greatest dysbiosis and reduces the microbial diversity by 40-60%, with increasing Streptococcus spp. two-to-threefold, and elevating antibiotic resistance gene prevalence. Cetylpyridinium chloride and polyhexamethylene biguanide showed milder effects, thus preserving 70-80% of commensals, while herbal and plant-based rinses (o-cymen-5-ol, StellaLife®, Rosella) reduced pathogens by 25-40% without disrupting the balance. Fluoride-arginine formulations promote beneficial bacteria by 30-50% but marginally upregulated resistance genes, whereas mechanical hygiene methods maintained over 90% microbial diversity. Suppression of nitrate-reducing bacteria was associated with reduced nitric oxide bioavailability, potentially increasing vascular and cognitive risks. Hence, antimicrobial mouthwashes especially chlorhexidine induces significant dysbiotic shifts, while herbal, postbiotic, and mechanical alternatives demonstrate safer, microbiome thereby preserving the effects which is suitable for long-term oral health maintenance.