Introduction: Silver diamine fluoride (SDF) is a simple and non-invasive agent used to arrest early childhood caries (ECC). This study aimed to investigate potential changes to the oral microbiome in children with ECC who were treated with SDF at three different frequency regimens. Methods: Forty-five children (n=15 per group) with ECC were recruited into a randomized clinical trial testing three different treatment frequency regimens of SDF. A total of 195 carious lesions were treated with two applications of 38% SDF and 5% sodium fluoride varnish (NaFV) and assessed over three study visits (one month (Regimen 1M), four months (Regimen 4M), or six months (Regimen 6M) apart). Dental plaque samples were collected at each visit. Sequencing of the V4-16S rRNA and ITS1 rRNA genes were used to study the supragingival plaque microbiome. Results: The overall arrest rates for treated carious lesions were 75.9% at Visit 2 and 92.8% at Visit 3. Arrest rates were higher for all lesions after two applications of SDF with NaFV, and applications one month and four months apart had higher arrest rates (95.9% and 98.5%) than six months (81.1%) apart. The microbial diversity analyses showed no significant differences in the overall microbiome after SDF treatment. However, significant changes in the abundance of specific bacteria and fungi, particularly Lactobacillus spp., Bifidobacterium spp., and Candida spp. were observed after treatment. Furthermore, overabundance of Streptococcus mutans and Candida dubliniensis at baseline was observed in children who had at least one caries lesion not arrested after one SDF application, compared to those who had 100% arrest rates. Conclusion: SDF with NaFV applications were an effective modality for arresting ECC, with higher arrest rates after two SDF applications. No loss of diversity but significant changes in the abundance of specific bacteria and fungi were consequences of SDF treatment.

The authors have declared no competing interest.

NCT04054635

Operating funds for this project were provided by the Children′s Hospital Research Institute of Manitoba and the Dr. Gerald Niznick College of Dentistry Endowment Fund. Dr. R.J. Schroth holds a Canadian Institute of Health Research Embedded Clinician Researcher Salary Award in ″Improving access to oral health care and oral health care delivery for at-risk young children in Manitoba″.

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The Biomedical Research Ethics Board of the University of Manitoba gave ethical approval for this work.

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Raw sequencing data produced in the present study are available upon reasonable request to the authors.