The landscape of the microbiome at different stages of root caries.

Objective: To investigate the relationship between microorganisms and root caries, identify core species, and explore their interactions.

Materials and methods: Thirty patients with different levels of root caries were included. Plaques from superficial (n = 30) and deep root caries (n = 30) and sound root surfaces (n = 30) were collected. Microbial diversity and composition across different stages of root caries were analyzed using 16 S rRNA and 18 S rRNA high-throughput sequencing. Wilcoxon paired comparisons were conducted to minimize individual variations. LefSe analysis was performed to identify stage-specific microbial enrichment. In vitro biofilm models of C. albicans, S. mutans and A. viscosus were established to examine the effects of C. albicans on biofilm formation, virulence factor expression, and metabolic pathway regulation. Fungal transcriptomes were sequenced to explore how fungal species affect bacterial growth and cariogenicity.

Results: No significant differences in microbial diversity or structure were observed, but relative abundances of some species differed significantly (p < 0.05). LefSe analysis showed that the genus Streptococcus, Actinomyces, Lactobacillus, and Bacillus were enriched in superficial caries, whereas Prevotella was enriched in deep lesions. C. albicans was the predominant fungal species in root plaques and positively correlated with S. mutans and Actinomyces sp. HMT448. C. albicans promoted the growth, biofilm formation, and cariogenicity of S. mutans and A. viscosus via the arginine biosynthesis pathway.

Conclusion: Oral microecology is stable, and species imbalance is a key factor in root caries. Cross-kingdom interactions between S. mutans, A. viscosus, and C. albicans enhance cariogenic biofilms via the arginine biosynthesis pathway, offering insights for clinical treatments of root caries.

Clinical relevance: Our study revealed the first landscape of the microbiome from different stages of root caries and indicated that targeting the interactions of core species may be a practical way to prevent and treat clinical root caries.