The oral microbiome associated with early childhood caries in preschool children: A scoping review

OBJECTIVE: This review compares the oral microbiota profiles of preschool children with early childhood caries (ECC) to those of caries-free controls. METHODS: PubMed, Web of Science, Embase, and Scopus were systematically searched for English-language reports published before January 1, 2026. Studies using next-generation sequencing (NGS) to compare the oral microbiota of systemically healthy preschool children (≤6 years) with and without ECC were included. Data on study characteristics, participant and sample information, study methods, and key study outcomes were extracted. Data were qualitatively synthesized, stratified by oral sample type and microbial kingdom. RESULTS: Twenty-one studies published between 2013 and 2025 were included. Some studies include overlapping sample types and microbial kingdoms, with three examining both plaque and salivary samples, and three analyzing both bacterial and fungal microbiota. Nine studies examined plaque bacterial microbiota. Eight reported no differences in alpha diversity between ECC-affected children and caries-free controls, whereas all studies reported significant differences in beta diversity between groups. Based on replication criteria, ten bacterial species were enriched and nine were depleted in ECC. Four studies examining plaque fungal microbiota yielded no consistent findings regarding fungal diversity, reflecting heterogeneity and limited replication across studies. However, two fungal species were found to be enriched in ECC in two studies. Twelve studies assessed salivary bacterial microbiota. Ten reported similar alpha diversity between ECC and control groups, while findings on beta diversity were inconsistent across studies. Based on replication criteria, four bacterial species were enriched in ECC and one was depleted. Three studies examined salivary fungal microbiota, with no consistent findings on fungal diversity and limited concordance between studies. CONCLUSION: This review indicates that bacterial communities exhibit similar species diversity between ECC-affected children and caries-free controls in both sample types. While plaque bacterial communities consistently differed in beta diversity and species abundance between the two groups, salivary bacterial communities show less consistent differences in beta diversity between ECC and controls. Fungal microbiota in both plaque and saliva remain understudied. CLINICAL SIGNIFICANCE: This review provided comprehensive evidence on the microbial features associated with ECC, highlighting stronger associations between plaque-specific dysbiosis and clinical caries status in preschool children.