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(1) Background: The aim of this study was to assess the preventive effect of tooth surface disinfection treatment, in addition to fluoride application, during fixed orthodontic treatment. (2) Methods: An open label randomized control trial for the evaluation of the dental caries preventive procedure was performed for the patients with high caries risk who had been visited at Department of Orthodontics, Tsurumi University Dental Hospital for orthodontics treatment. The follow-up period was six months. White spot lesions (WSLs) were evaluated by quantitative light-induced fluorescence (QLF). Cariogenic bacteria were monitored and evaluated by bacterial culture. In addition, the oral microbiome was evaluated by a next-generation sequence (NGS). (3) Results: By the mixed effect modeling, tooth surface disinfection treatment significantly reduced cariogenic bacteria and all parameters obtained by QLF. (4) Conclusions: Tooth surface disinfection treatment, in addition to PMTC and fluoride application, were effective for dental caries prevention and keeping a healthy microbiome during orthodontic treatment.

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