Multiniche mycobiome profiling identifies distinctive fungal dysbiosis in common variable immunodeficiency

Common variable immunodeficiency (CVID) is associated with bacterial dysbiosis, particularly in patients with immune dysregulation, but the contribution of the fungal microbiome (mycobiome) remains poorly understood.

We conducted a cross-sectional, multi-compartment study in 41 adults with CVID (24 with immune dysregulation, dCVID; 17 with infectious-only manifestations, iCVID) and 15 matched healthy controls. Saliva, sputum and stool samples were analyzed using ITS1 amplicon sequencing with amplicon sequence variant-based taxonomic assignment, followed by α/β-diversity analyses, multivariate modeling, differential abundance testing and machine learning approaches for biomarker identification.

Across all three niches, mycobiome composition differed significantly between CVID and controls, whereas dCVID and iCVID did not separate. Fungal richness and evenness were reduced in CVID, most prominently in respiratory and oral samples. ANCOM-BC revealed a reproducible "Candida-skewed" configuration in both phenotypes, with marked enrichment of Candida albicans in sputum, stool and saliva, accompanied by increased abundance of other opportunistic yeasts such as Nakaseomyces glabratus. In contrast, environmental or putatively commensal taxa were consistently depleted. Random forest models based on fungal profiles accurately discriminated CVID from controls, with AUC up to 0.96 (95% CI 0.91-0.99) in saliva and 0.94 (95% CI 0.88-0.99) in stool, whereas classification of dCVID versus iCVID was modest.

Together, these findings provide the first integrated view of mycobiome alterations across multiple ecological niches in CVID, highlighting consistent enrichment of opportunistic yeasts over commensals. The expansion of C. albicans supports a potential pathobiont role, and the strong discriminatory performance of fungal signatures underscores their promise as non-invasive biomarkers in this immunodeficiency.