Journal Article

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

Li, Chen, Guo, Xiaonan, Ji, Xiaolei, Lv, Jialin, Li, Hongge, Miao, Beibei, Zhou, Zixing, Du, Yu, Guo, Chen, Geng, Yuanyuan, Hu, Yijie, Gong, Jie, Sun, Yihua, Zhang, Shu

2026

Overview

Objectives 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. Methods 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. Results 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. Conclusions 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. Clinical register number Not applicable.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: 16S rRNA sequencing / Adult / Analysis / Antiretroviral agents / Antiretroviral drugs / Antiretroviral therapy / Antiviral agents / Bacteria / Bacteria - classification / Bacteria - genetics / Bacteria - isolation & purification / Biological diversity / Biomarkers / Candida / Candidiasis / CD4 antigen / CD4 Lymphocyte Count / Community structure / Composition / Datasets / Drug therapy / Dysbacteriosis / Dysbiosis / Dysbiosis - immunology / Dysbiosis - microbiology / Female / Fungi / Fungi - classification / Fungi - genetics / Fungi - isolation & purification / Health aspects / Health risks / Highly active antiretroviral therapy / HIV / HIV (Viruses) / HIV infection / HIV Infections - complications / HIV Infections - immunology / HIV Infections - microbiology / HIV patients / Human immunodeficiency virus / Humans / Hypothesis testing / Immune status / Immunosuppression / Immunosuppression Therapy / Immunotherapy / Infection / Infections / Infectious Diseases / Internal Medicine / Kruskal-Wallis test / Lymphocytes / Lymphocytes T / Male / Medical Microbiology / Medical research / Medicine / Medicine & Public Health / Medicine, Experimental / Microbiomes / Microbiota / Microbiota (Symbiotic organisms) / Microorganisms / Middle Aged / Mortality / Parasitology / Pathogens / Pharyngeal microbiome / Pharynx / Pharynx - microbiology / Physiological aspects / Risk factors / RNA / RNA, Ribosomal, 16S - genetics / rRNA 16S / T cells / Throat / Tropical Medicine / Variables / Variance analysis