Limited impact of HIV infection and immune status on the gut mycobiota

A growing body of literature connects the gut mycobiota to several diseases, including HIV infection. In contrast to bacteria, fungi represent a smaller fraction of the gut microbiota and pose several technical challenges, including low biomass, environmental contamination and primer-associated biases. Characterizing the gut mycobiota in HIV infection is still at an early stage. We characterized the gut mycobiota in untreated people living with HIV (PWH, n = 69), PWH on antiretroviral therapy (PWHA) for at least 2 years (n = 14) and people without HIV (PWoH, n = 48) using ITS1 sequencing, which preferentially detects certain fungal taxa such as Candida. Associations with immune status (CD4 count), fungal (1,3-β-D-glucan) and bacterial translocation (soluble CD14), monocyte activation (sCD163) and epithelial integrity (intestinal fatty acid binding protein, I-FABP) were assessed. Analyses included diversity metrics, differential abundance, and correlations, acknowledging potential residual confounders. Fungal diversity (richness and Shannon index) did not differ significantly between groups, although PWH with CD4 ≥ 200 cells/µL showed values closer to PWHA and PWoH. Immune status explained a small but significant proportion of the variance in fungal composition (6.2%, P = 0.002). The gut mycobiota was dominated by Candida (18.6%), Aspergillus (18.2%), Rhodotorula (11.5%), Penicillium (8.1%), and Saccharomyces (7.5%), taxa that might partly reflect dietary or environmental exposures. Four enterotypes, dominated by Aspergillus, Saccharomyces, Rhodotorula, and Candida were identified; the Candida-dominated enterotype was less diverse (P < 0.01), observed only in PWH, and associated with lower CD4 counts and higher sCD163 levels. Consistently, Candida relative abundance was inversely correlated with CD4 counts, CD4/CD8 ratio, and positively with sCD163. Enterotype stratification did not reveal consistent associations with other host metadata. Circulating 1,3-β-D-glucan levels did not differ between groups. HIV infection and immune status are associated with specific fungal signatures, including a Candida-dominated enterotype linked to CD4 counts and monocyte activation, although overall effects are modest relative to high inter-individual variability. Interpretation is limited by residual confounding, particularly diet and environmental exposures, ITS1-related biases, and cohort composition enriched for advanced HIV. These findings support the need for integrative, longitudinal studies to clarify the role of the gut mycobiota in HIV.