The impact of HIV on the oral microbiome of children living in Sub-Saharan Africa using a rpoC gene-fragment metataxonomic approach

Children living with HIV (CLWH) have a higher prevalence of oral diseases including caries, the mechanisms of which are not well understood. Here, we test the hypothesis that CLWH have a more cariogenic oral microbiome characterized by an increase in bacteria involved in the pathogenesis of caries. We present data generated from supragingival plaques collected from 484 children representing three exposure groups: (1) children living with HIV (HI), (2) children who were perinatally exposed but uninfected (HEU), and (3) unexposed and therefore uninfected children (HUU). We found that the microbiome of CLWH is distinct as compared to HEU or HUU children, and that this distinction is more pronounced in diseased teeth as compared to healthy teeth, suggesting that the impact of HIV is more severe as caries progresses. Moreover, we report both an increase in bacterial diversity and decrease in community similarity in older CLWH as compared to younger CLWH which may in part be a prolonged effect of HIV and/or its treatment. Finally, while Streptococcus mutans is often a dominant species in late-stage caries, it tends to be found at lower frequency in late-stage caries of CLWH as compared to other groups. Our results highlight the taxonomic diversity of the oral microbiome and suggest that broad and increasingly individualistic ecological shifts are responsible for the pathogenesis of caries in CLWH coupled with a diverse and possibly severe impact on known cariogenic taxa that potentially exacerbates caries.