Fungal-bacterial gut microbiota interactions in patients with Clostridioides difficile colonisation and infection

ObjectivesThe bacterial microbiota is well-recognised for its role in Clostridioides difficile colonisation and infection, while fungi and yeasts remain understudied. The aim of this study was to analyse the mycobiota and its interactions with the bacterial microbiota in light of C. difficile colonisation and infection. MethodsThe mycobiota was profiled by ITS2 sequencing of faecal DNA from infected patients (CDI; n = 29), asymptomatically colonised patients (CDC; n = 38) and hospitalised controls with C. difficile negative stool culture (Controls; n = 38). Previously published 16S rRNA gene sequencing data of the same cohort were used additionally for machine learning and fungal-bacterial network analysis. ResultsCDI patients were characterised by a significantly higher abundance of Candida spp. (MD 0.270 {+/-} 0.089, P = 0.002) and Candida albicans (MD 0.165 {+/-} 0.082, P = 0.023) compared to Controls. Additionally, they were deprived of Aspergillus spp. (MD -0.067 {+/-} 0.026, P = 0.000) and Penicillium spp. (MD -0.118 {+/-} 0.043, P = 0.000) compared to CDC patients. Network analysis revealed a positive association between several fungi and bacteria in CDI and CDC, although the analysis did not reveal a direct association between Clostridioides spp. and fungi. Furthermore, the microbiota machine learning model outperformed the models based on the mycobiota and the joint microbiota-mycobiota model. The microbiota classifier successfully distinguished CDI from CDC (AUROC = 0.884) and CDI from Controls (AUROC = 0.905). Blautia and Bifidobacterium were marker genera associated with CDC patients and Controls. ConclusionsThe gut mycobiota differs between CDI, CDC, and Controls, and may affect Clostridioides spp. through indirect interactions. The identification of bacterial marker genera associated with CDC and Controls warrants further investigation. Although the mycobiotas predictive value of C. difficile status was low, fungal-bacterial interactions might be considered when diagnosing and treating C. difficile infection.