Analysis of pharyngeal microbiome characteristics in HIV-infected individuals: correlation between the degree of immunosuppression and microbial dysbiosis

Despite the significant improvement in survival rates due to antiretroviral therapy, opportunistic infections continue to pose a major health risk for individuals living with HIV. As a key anatomical intersection of the upper respiratory and digestive tracts, the pharyngeal microbiome during HIV infection remains poorly characterized. This study aimed to compare the composition of bacterial and fungal communities in the pharynx between HIV-infected individuals and healthy controls, and to investigate their association with host immune status. Throat swab samples were collected from 70 HIV-infected individuals—stratified into severe, moderate, and no/mild immunosuppression groups based on CD4⁺ T-cell counts—and 18 healthy controls. Microbial composition was assessed using 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing. Bacterial alpha diversity was significantly reduced in the severe immunosuppression group (CD4⁺ T cells < 200/µL) compared to other groups, whereas fungal alpha diversity did not differ significantly across groups. Beta-diversity analysis revealed a distinct bacterial community structure in the severe immunosuppression group. Fungal communities, however, differed significantly between all HIV-infected individuals and healthy controls. At the genus level, the severe immunosuppression group exhibited a decrease in commensal bacteria such as Prevotella and an increase in Halomonas. Additionally, Candida was significantly enriched in the severe immunosuppression group, while Exophiala levels were elevated across all HIV-infected groups. The pharyngeal microbiome of HIV infected individuals undergoes significant changes, with bacterial community disorder associated with immune suppression, while the fungal community changes are more closely related to the HIV infection status of the individuals. The enrichment of Candida in individuals with severe immune suppression is more appropriately interpreted as a manifestation of fungal dysbiosis associated with advanced immunosuppression and a potential indicator of increased susceptibility to oropharyngeal candidiasis, rather than as a diagnostic biomarker of overt disease. Not applicable.