Oral Microbiome and Dental Caries in Kenyan Children and Adolescents Living with HIV

This cross-sectional study evaluates the association between the oral microbiome and the presence of untreated dental caries among Kenyan children and adolescents living with HIV (CALHIV).

We collected 83 oral swab samples from CALHIV receiving medical care at Kenyatta National Hospital. We used the 16S rRNA sequencing technique on oral swab samples to profile bacterial composition. Only CALHIV with results of oral microbiome and dental examinations simultaneously were included in the further analysis. We compared the alpha and beta diversity of the oral microbiome between individuals with and without dental caries. Log-ratio LASSO regression with 2-stage estimation, 10-fold cross-validation, and adjustment for the false discovery rate was applied to select the best features that can predict caries status at the phylum level.

Of the 70 participants with both oral health data and oral microbiome data available, 66% had dental caries. The group with dental caries had higher Chao 1 alpha diversity (P = 0.046) but not beta diversity. Log-ratio LASSO regression had a higher ratio of paired features proteobacteria/SR1 (P = 0.0067), Euryarchaeota/SR1 (P = 0.0074), Acidobacteria/SR1 (P = 0.0079), and Fusobacteria/SR1 (P = 0.0125) at the phylum level and was significantly associated with a lower prevalence of untreated dental caries. A higher abundance of SR1 together with certain bacteria was associated with a higher prevalence of untreated dental caries.

This is the first study to analyze the oral microbiome of CALHIV and untreated dental caries in a cohort that had received medical care since their first years of life. While this study provides information about the paired feature selection for dental caries in CALHIV on ART using cross-validation, SR1 may interact with other bacteria to increase the prevalence of untreated dental caries. Longitudinal microbiome data and samples from multiple sites in the oral cavity will be essential for understanding and confirming these findings.Knowledge Transfer Statement:The results of this study can help clinicians understand how SR1 interacts with other bacteria that may increase the prevalence of untreated dental caries in children and adolescents living with HIV and on long-term antiretroviral therapy. Furthermore, these findings may provide valuable insights for future research, informing longitudinal microbiome data and sampling from various sites in the oral cavity.