Oral Viral Signatures In Caries: Metagenome-Based Virome Analysis

The study aimed to identify the oral viral signatures of patients with caries and to elucidate the potential of these viral markers for assessing disease risk in diagnosis and therapy. A total of 57 usable saliva (containg 34 caries patients and 23 healthy controls) and 142 supragingival plaque (containg 95 caries patients and 47 healthy controls) metagenomes were obtained from six published caries studies. An oral viral catalog was constructed using a reference-dependent approach. We then screened vOTUs with significant differences and performed viral genomics analysis and virus host assignment. The oral virome composition varies in caries patients, though α-diversity trends differ across datasets due to individual differences. Notably, viral α-diversity strongly correlates with bacterial α-diversity, suggesting broad virus-bacteria interactions. Regardless of disease status or sampling site, most oral viruses belong to Siphoviridae, Myoviridae, Podoviridae, and Autographiviridae. Principal coordinate analysis revealed significant virome compositional differences between datasets, with disease state having a pronounced effect. Further analysis identified 135 vOTUs with significant difference in children’s supragingival plaque, 393 in adults’ supragingival plaque, and 362 in adults’ saliva. Host assignment further revealed a complex phage-bacteria interaction network. Genomic analysis showed these phages encode auxiliary genes linked to carbohydrate metabolism, antibiotic resistance, and immune regulation, potentially enhancing host survival and pathogenicity. Our findings confirm the oral virome characteristics of caries and highlight the synergistic role of oral virus-bacteria in the progression of caries. Bacteriophages of caries may be a new target for treatment.