Candida species overgrowth in the human gut is considered a prerequisite for invasive
candidiasis, but our understanding of gut bacteria promoting or restricting this overgrowth
is still limited. By integrating cross-sectional mycobiome and shotgun metagenomics
data from the stool of 75 male and female cancer patients at risk but without systemic
candidiasis, bacterial communities in high Candida samples display higher metabolic
flexibility yet lower contributional diversity than those in low Candida samples.
We develop machine learning models that use only bacterial taxa or functional relative
abundances to predict the levels of Candida genus and species in an external validation
cohort with an AUC of 78.6-81.1%. We propose a mechanism for intestinal Candida overgrowth
based on an increase in lactate-producing bacteria, which coincides with a decrease
in bacteria that regulate short chain fatty acid and oxygen levels. Under these conditions,
the ability of Candida to harness lactate as a nutrient source may enable Candida
to outcompete other fungi in the gut.
