Fungal and Bacterial Gut Microbiota Differ Between Colonization and Infection

The bacterial microbiota is well-recognized for its role in colonization and infection, while fungi and yeasts remain understudied. The aim of this study was to analyze the predictive value of the mycobiota and its interactions with the bacterial microbiota in light of colonization and infection. The mycobiota was profiled by ITS2 sequencing of fecal DNA from infection (CDI) patients ( = 29), asymptomatically colonization (CDC) patients ( = 38), and hospitalized controls with negative stool culture (controls; = 38). Previously published 16S rRNA gene sequencing data of the same cohort were used additionally for machine learning and fungal-bacterial network analysis. CDI patients were characterized by a significantly higher abundance of spp. (MD 0.270 ± 0.089, = 0.002) and (MD 0.165 ± 0.082, = 0.023) compared to controls. Additionally, they were deprived of spp. (MD -0.067 ± 0.026, = 0.000) and spp. (MD -0.118 ± 0.043, = 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 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 [Area Under the Receiver Operating Characteristic (AUROC) = 0.884] and CDI from controls (AUROC = 0.905). and were marker genera associated with CDC patients and controls. The gut mycobiota differs between CDI, CDC, and controls and may affect spp. through indirect interactions. The mycobiota data alone could not successfully discriminate CDC from controls or CDI patients and did not have additional predictive value to the bacterial microbiota data. The identification of bacterial marker genera associated with CDC and controls warrants further investigation.