Mycobiota dynamics in inflammatory bowel disease: Fungal biomarkers and Clostridioides difficile co-infection

This study aimed to characterize the fecal fungal microbiota in inflammatory bowel disease (IBD) patients, with and without Clostridium difficile infection (CDI), compared to healthy controls (HC).

ITS sequencing assessed fungal composition and diversity in fecal samples from 139 IBD patients (45 with CDI) and 35 HC. Key fungal taxa were identified through random forest modeling, with ROC curves evaluating their diagnostic potential. Correlations between fungal microbiota and clinical parameters were analyzed.

IBD patients showed reduced fungal α-diversity compared to HC, with significant β-diversity differences among CDI-IBD, non-CDI IBD, and HC groups. Saccharomyces was elevated in IBD patients, while Bipolaris was lower than in HC. Random forest analysis showed strong classification performance, with AUCs of 93.7 % for distinguishing non-CDI IBD from HC, and 82.2 % for CDI-IBD from non-CDI IBD. Penicillium was negatively correlated with WBC and CRP, Candida with fecal calprotectin, and Bipolaris positively with BMI.

Significant fungal dysbiosis was observed in IBD, with potential diagnostic implications for gut fungi in IBD and CDI. The study also highlights correlations between gut fungi and clinical parameters, which may guide targeted diagnosis and treatment.