Characterization of Supragingival Plaque and Oral Swab Microbiomes in Children With Severe Early Childhood CariesOriginal paper
Karen Pendergrass is a microbiome researcher specializing in microbiome-targeted interventions (MBTIs). She systematically analyzes scientific literature to identify microbial patterns, develop hypotheses, and validate interventions. As the founder of the Microbiome Signatures Database, she bridges microbiome research with clinical practice. In 2012, based on her own investigative research, she became the first documented case of FMT for Celiac Disease, four years before the first published case study.
Read MoreWhat was studied?
This study compared two oral sampling methods, supragingival dental plaque and oral swabs, to see which better predicts severe early childhood caries (S-ECC) versus caries-free status. Researchers used next generation sequencing of the V4-16S rRNA gene (bacteria) and the ITS1 rRNA gene (fungi) to characterize the microbiome and mycobiome at each site. They then applied machine learning to build classification models from the resulting sequencing data.
Who was studied?
The cohort consisted of 80 children under 72 months of age, recruited in a cross-sectional design. Of these, 40 children had severe early childhood caries and 40 were caries-free controls. Both dental plaque and oral swab samples were collected from each child, allowing paired comparison of the two sampling sites within the same population.
What were the most important findings?
Dental plaque and oral swab samples showed significantly different alpha and beta diversity for both bacterial and fungal microbiomes. The cariogenic bacterium Streptococcus mutans was more abundant in dental plaque than in oral swabs among children with S-ECC. The fungal species Candida dubliniensis and C. tropicalis were more abundant in oral swab samples from children with S-ECC compared to caries-free controls, and these fungal taxa ranked among the top 20 features for classifying S-ECC status and for distinguishing sample type within the S-ECC group.
What are the greatest implications of this study?
The findings suggest that sampling site meaningfully changes which microbial and fungal signals are detected, so plaque and swab samples are not interchangeable for caries research. The prominence of Candida dubliniensis and C. tropicalis in oral swabs points to a fungal, not just bacterial, contribution to severe early childhood caries that could be missed if only plaque is sampled. Combining sampling-site-aware sequencing with machine learning may improve early prediction models for pediatric caries risk.