Candidaspecies 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 highCandidasamples display higher metabolic flexibility yet lower contributional diversity than those in lowCandidasamples. We develop machine learning models that use only bacterial taxa or functional relative abundances to predict the levels ofCandidagenus and species in an external validation cohort with an AUC of 78.6–81.1%. We propose a mechanism for intestinalCandidaovergrowth 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 ofCandidato harness lactate as a nutrient source may enableCandidato outcompete other fungi in the gut.