Gut microbial community patterns are associated with HIV-related host parameters in a Prevotella- and Saccharomyces-rich cohort

Despite effective viral suppression with modern antiretroviral therapy, HIV remains a chronic condition with lasting systemic effects, including significant impacts on gut microbial ecology. We analyzed fecal bacterial (16S rRNA gene) and fungal (ITS) profiles from 94 men with HIV—the largest cohort of its kind in the Czech Republic—to determine how antiretroviral therapy (ART) regimen, treatment duration, and blood parameters shape gut microbiome diversity and composition. The bacteriome was dominated by Bacillota and Bacteroidota. Prevotella was the most abundant bacterial genus, while several genera commonly associated with SCFA production, including Faecalibacterium , were also detected. The mycobiome showed marked inter-individual variability, with Saccharomyces as the dominant genus. Ecological network analysis identified descriptive differences in microbial interactions between ART-duration groups, with a more interconnected network observed in participants with shorter ART duration. In addition, bacterial alpha diversity differed significantly according to ART duration. Several Prevotella -related taxa and members of the Lachnospiraceae family were associated with viral load, while triglyceride levels correlated with taxa including Alloprevotella and Prevotella 9. Overall, our findings suggest that differences associated with ART duration may be more apparent in microbial co-occurrence patterns than in overall taxonomic community composition.