Genomic comparison of chlorhexidine, fluoride, and probiotic mouthwashes on oral microflora in fixed orthodontic patients

Objectives: To compare the effects of chlorhexidine, fluoride, and probiotic mouthwashes on selected oral microorganisms in patients undergoing fixed orthodontic treatment using polymerase chain reaction (PCR) and genome sequencing. Material and Methods: Eighty patients aged 13–29 years undergoing fixed orthodontic treatment were randomly allocated to four groups of 20 each: Chlorhexidine mouthwash, fluoride mouthwash, probiotic mouthwash, and control. Participants in the intervention groups brushed twice daily with fluoridated toothpaste and rinsed twice daily with the assigned mouthwash diluted 1:1 with water for 60 s for 30 days. The control group used toothbrushing and water rinsing only. Plaque samples were collected from the first premolar bracket area after 30 days. Microbial genomic DNA was extracted, and PCR was performed to detect Streptococcus mutans, Lactobacillus acidophilus , and porphyromonas gingivalis . One amplified sample per group for each bacterium underwent genome sequencing. Categorical comparisons were analyzed using the Chi-square test, with statistical significance set at p < 0.05. Results: The control group showed the highest prevalence of all three microorganisms. S. mutans positivity was highest in the control group (80%) and lowest in the fluoride group (20%). L. acidophilus positivity was highest in the control group (50%) and lowest in the chlorhexidine group (15%). P. gingivalis positivity was highest in the control group (55%) and lowest in the chlorhexidine group (15%). Intergroup differences were statistically significant for S. mutans and P. gingivalis . Chlorhexidine, fluoride, and probiotic mouthwashes all reduced microbial prevalence compared with the control group. Conclusion: Adjunctive mouthwash use during fixed orthodontic treatment reduced oral microbial prevalence compared with toothbrushing alone. Chlorhexidine showed the greatest reduction in P. gingivalis and L. acidophilus , while fluoride showed the greatest reduction in S. mutans . Probiotic mouthwash demonstrated a moderate antimicrobial effect and may be considered a useful adjunct to routine oral hygiene measures.