High-resolution microbial changes in root caries revealed by Type IIB Restriction-site associated DNA for microbiome

This study aimed to characterize the species-level microbial and functional alterations in the dental biofilms associated with root caries leveraging the high-resolution sequencing.

Twenty-five older adults with active root caries (Patients) and 31 older adults without untreated caries (Healthy controls) were enrolled. Site-specific supragingival plaque was collected from spatially-matched carious (CC) and caries-free (CH) root surfaces from patients, and from caries-free root surfaces of healthy controls (HH). Plaque samples were analysed using Type IIB Restriction-site Associated DNA for Microbiome (2bRAD-M). Microbial diversity, species-level relative abundance, and predicted functional pathways were compared across groups using nonparametric tests.

No significant differences in overall microbial diversity were observed between groups. The microbial divergence between paired carious (CC) and caries-free (CH) root microbiota from patients was significantly greater than that between paired caries-free (HH) root microbiota in healthy controls. Several species showed increased abundance in CC microbiota compared to CH microbiota, with Propionibacterium acidifaciens, Prevotella multisaccharivorax, Mitsuokella sp000469545, and Parascardovia denticolens exhibiting the highest level of abundance difference. Predicted metagenomic analysis indicated that nine KEGG pathways, primarily involved in alternative carbohydrate metabolism, were positively associated with root caries status.

Within-subject comparison revealed a significant difference in microbiota between carious and caries-free root surfaces. These differences were characterized by shifts in specific species and their associated metabolic potentials, rather than by broad changes in community diversity.

This study underscores the importance of tooth-level resolution in investigating the microbial etiology of root caries and revealed the species-level changes in carious root microbiota.