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Background:  This study investigated the microbial changes during treatment with clear aligners (CA) and fixed appliances (FA) and evaluated the utility of saliva as a diagnostic marker in orthodontic patients. Methods:  Ten patients each were enrolled in the FA and CA groups. Plaque (PI) and gingival indices (GI) were measured at baseline, three, six and 12 months. Saliva and plaque samples were collected at each time point for determination of the respective microbial community composition via 16S rRNA sequencing. Results:  PI and GI increased significantly over time only in FA patients. While alpha diversity was similar for FA or CA patients, beta diversity and microbial community composition analysis revealed significant differences between saliva and plaque for both treatment groups. Further analysis of the relative abundance of certain health- and disease-associated genera present in the saliva and plaque of FA and CA patients correlated with the clinical parameters. Conclusions:  Clinical parameters significantly worsened during orthodontic treatment with FA but not CA. The microbial composition of plaque and saliva differed significantly between treatment groups. However, the changes in abundance of some individual genera were similar in both saliva and plaque in correlation with the corresponding clinical parameters. These genera show potential as biomarkers for health and disease. Practical implications:  Monitoring of the microbial community composition during orthodontic treatment could reduce the risk of oral disease development. While the microbial composition of saliva is not reflective of the plaque communities implicated in oral health and disease, individual marker genera show promise as biomarkers.

Salivary and Plaque Microbiomes During Treatment With Different Orthodontic Appliances