The oral microbiome of root caries: A scoping review

Abstract

Objective: This review characterizes shifts of the oral microbial community on carious root surfaces compared to sound root surfaces. Data and sources: A systematic search of English-language publications on clinical studies evaluating oral microbiomes in patients with root caries using high-throughput sequencing technologies published before April 1, 2025, was included. The search was conducted on PubMed, Cochrane Central Register of Controlled Trials, Web of Science, Embase, and Scopus. Gray literature was searched in ClinicalTrials.gov and Google Scholar. Study selection/Results: Based on the eligibility criteria, 1133 publications were screened, and 465 duplicates were removed. Of the remaining 16 studies assessed for full-text review, eight investigating the oral microbiome of saliva, carious roots, or dental plaque in patients with root caries were included. These studies reported the intra-community species diversity (alpha-diversity, 4/8 studies), inter-community compositional diversity (beta-diversity, 4/8 studies), dominant microbial genera/species (8/8 studies), and functional pathways (1/8 studies) of the microbial community in root caries patients. Alpha-diversity showed no significant difference between root caries and sound root surfaces in three studies, but root caries exhibited a significantly lower alpha diversity in one study. Beta-diversity differed significantly between root caries and sound root surfaces in three studies, with one study reporting no difference. The dominant microbial species in root caries varied among the included studies. However, Lactobacillus spp., Prevotella denticola, Propionibacterium acidifaciens, Streptococcus mutans, and Veillonella parvula/dispar were frequently identified in the root caries-associated microbiota. Furthermore, root caries-associated bacteria altered the predicted functional pathways, promoting organic acid production and accelerating collagen degradation. Conclusion: Root caries microbiomes exhibit distinct compositional profiles, dysbiotic species predominance, and a shift in predicted functional pathways compared to healthy root surfaces. Clinical significance: This review provides valuable insights into root caries’ microbial landscape, potentially guiding future preventative and therapeutic strategies.