Introduction: The design of the orthodontic bracket or appliance is 1 of the most important factors for creating retentive areas for biofilm formation. In orthodontics, this would be the first study to compare the microbial level changes in 3 different types of orthodontic appliances using checkerboard DNA-DNA hybridization technique. The purpose of this study was to evaluate and compare the extent of appearance of orange and red microbial complexes in patients undergoing orthodontic treatment using aligners, conventional metallic fixed labial appliances, and lingual fixed appliances. Methods: A total of 60 patients, of which 20 patients were undergoing treatment with aligners, 20 patients with labial fixed appliances, and 20 patients with lingual fixed appliances, were included in our study. After 30 days, debonded brackets and rinsed aligners were stored and processed for analysis with checkerboard DNA-DNA hybridization. Results: Most bacterial species showed moderate counts, with the exception of Treponema denticola, which showed a higher count in all 3 types of appliances. Fusobacterium nucleatum, Porphyromonas gingivalis, and T denticola were present in a higher percentage in the lingual appliance. Fusobacterium periodontium and Prevotella intermedia were present in a higher percentage in the labial fixed appliance. Campylobacter rectus, Tannerella forsythia, and Prevotella melaninogenica counts were moderate in all 3 appliances, with the first 2 microbes showing slightly higher counts in aligners. The association between all the microorganisms were statistically insignificant, with the exception of F nucleatum, which showed a strong statistically significant association in all 3 types of appliances. Conclusions: The microbial contamination in metallic brackets was higher than that of aligners, when used for a month. Lingual fixed appliances showed more microbial contamination than labial fixed appliances followed by aligners.

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