Effects of Antiseptic Formulations on Oral Microbiota and Related Systemic Diseases: A Scoping Review

Background: Oral antiseptic formulations are widely used as adjuncts in oral hygiene to reduce pathogenic microorganisms and prevent oral diseases. While these agents are effective in controlling biofilm, their broader effects may disrupt the oral microbiota’s balance, potentially contributing to systemic health implications. The complex relationship between antiseptic use, microbial composition, and systemic outcomes remains insufficiently mapped. Objective: This scoping review aimed to explore and map the current evidence regarding the impact of antiseptic formulations on oral microbiota composition and to examine their potential associations with systemic diseases. Methods: A comprehensive literature search was performed using PubMed, Scopus, and Web of Science up to June 2025. Studies were included if they investigated antiseptic formulations commonly used in oral healthcare—such as chlorhexidine, essential oils, and cetylpyridinium chloride—and reported effects on oral microbiota and/or systemic health. Eligible study types included human clinical trials, observational studies, in vitro, and animal studies. Two reviewers independently screened and selected studies, with disagreements resolved by consensus. Data extraction focused on study design, antiseptic agents, microbial outcomes, and systemic implications. A total of 12 studies were included and charted. Results: The included studies demonstrated that oral antiseptics effectively reduce pathogenic microorganisms and improve clinical outcomes in oral diseases such as gingivitis and periodontitis. However, several studies also reported alterations in commensal microbial communities, suggesting a potential for dysbiosis. Some studies indicated possible links between antiseptic-induced microbial changes and systemic conditions, including cardiovascular and respiratory diseases. Conclusions: The evidence highlights a dual effect of antiseptic formulations: while beneficial in controlling oral pathogens, they may disrupt microbial homeostasis with possible systemic consequences. Further research is needed to evaluate long-term effects and develop targeted, microbiota-preserving oral hygiene strategies.