Metabolic Cross-Feeding Supports Growth of Candida albicans and Enterococcus faecalis in the Gut Microbiome

The fungal species Candida albicans and the bacterium Enterococcus faecalis are both common members of the gut microbiome, with co-occurrence of these two species widely reported in dysbiotic gut environments. While prior research suggests these species interact in the gut, the underlying mechanisms of these interactions remain unclear. To explore these interactions further, we utilized dual RNA-sequencing to transcriptionally profile both C. albicans and E. faecalis during co-culture and mono-culture under two conditions: (1) an in vitro condition designed to mimic certain aspects of the gut environment and (2) the germ-free mouse gut. Gene expression analysis revealed that both species strongly upregulate citrate-related genes during co-culture: C. albicans upregulates CIT1 (citrate synthase) which produces citrate, while E. faecalis upregulates its cit operon, responsible for citrate metabolism. In vitro co-cultures revealed that citrate cross-feeding supports increased growth of E. faecalis, which depends both on C. albicans' expression of CIT1 and E. faecalis' expression of the cit operon. A main byproduct of citrate metabolism in E. faecalis is formate, a short chain fatty acid (SCFA) toxic to fungi. Our RNA profiling revealed that C. albicans strongly upregulates three formate dehydrogenases (FDHs) during co-culture, enabling formate detoxification and conferring a growth advantage to C. albicans when grown in E. faecalis conditioned medium. These findings reveal a metabolically driven interaction between C. albicans and E. faecalis in the gut, where cross-feeding of citrate and detoxification of formate facilitates the growth of both species when they are cultured together. Using a simplified fungal-bacterial co-culture system, our studies begin to reveal the mechanistic complexities of metabolic sharing between a eukaryote and a bacterium.