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This study aimed to investigate potential changes to the oral microbiome in children with ECC who were treated with SDF and sodium fluoride (NaF) varnish at three different frequency regimens.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Forty-five children (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200915 per group) with ECC were recruited from community-based dental clinics in Winnipeg, Canada into an open-label, parallel-group, 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% NaF varnish (and assessed over three study visits one month, four months, or six months apart. Dental plaque samples were collected at each visit. Sequencing of the V4-16\u00a0S rRNA and ITS1 rRNA genes were used to study the supragingival plaque microbiome.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:italic>Lactobacillus<\/jats:italic>\n                      spp.,\n                      <jats:italic>Bifidobacterium<\/jats:italic>\n                      spp., and\n                      <jats:italic>Candida<\/jats:italic>\n                      spp., were observed after treatment. Furthermore, overabundance of\n                      <jats:italic>Streptococcus mutans<\/jats:italic>\n                      and\n                      <jats:italic>Candida dubliniensis<\/jats:italic>\n                      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. The overall arrest rates for treated carious lesions were 75.9% at the second visit and 92.8% at the third visit. Arrest rates were higher for all lesions after two applications of SDF with NaF varnish, and applications one month and four months apart had higher arrest rates (95.9% and 98.5%) than six months (81.1%) apart.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Applications of SDF with NaF varnish were an effective modality for arresting ECC, with higher arrest rates after two SDF applications. No loss of diversity but changes in the abundance of specific bacteria and fungi were observed after SDF treatment.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Trial registration<\/jats:title>\n                    <jats:p>ClinicalTrials.gove NCT04054635 (first registered 13\/08\/2019).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12903-025-06986-0","type":"journal-article","created":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T10:28:52Z","timestamp":1761042532000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Effects of silver diamine fluoride on oral bacteriome and mycobiome: a randomized clinical trial"],"prefix":"10.1186","volume":"25","author":[{"given":"Mayura","family":"Manerkar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vivianne Cruz","family":"de Jesus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Betty-Anne","family":"Mittermuller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor H. 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