UCSF

The adult gut microbiome is a diverse community of thousands of microorganisms spanning all three kingdoms of life. In contrast, the infant gut microbiome is relatively simple, offering a powerful, biologically relevant system to study foundational microbial community interactions. The fungal species Candida albicans and the bacterium Enterococcus faecalis are both common members of the infant gut microbiome, with co-occurrence of these two species widely reported across various dysbiotic gut environments. While previous studies suggest that C. albicans and E. faecalis interact in the gut, the mechanisms behind these interactions remain unclear. To more deeply probe the interaction between C. albicans and E. faecalis in the gut, we used dual RNA-sequencing to profile the transcriptional responses of both organisms during co-culture and compared them to individual growth 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 of revealed that both species strongly upregulate citrate-related genes in each other’s presence: C. albicans upregulates CIT1 (citrate synthase) which produces citrate, while E. faecalis upregulates the entire cit operon, responsible for citrate metabolism. In in vitro co-cultures, we show that citrate is produced and secreted from C. albicans and consumed by E. faecalis, revealing a cross-feeding interaction. We further show that this citrate cross-feeding supports increased growth of E. faecalis, which depends on both C. albicans' expression of CIT1 and E. faecalis' expression of the cit operon. Formate, a Short Chain Fatty Acid (SCFA) known to be toxic to fungi, is a byproduct of citrate metabolism in E. faecalis. Indeed, we observed higher formate secretion from E. faecalis strains capable of metabolizing citrate. Our RNA profiling revealed that C. albicans strongly upregulates three formate dehydrogenases (FDHs) when co-cultured with E. faecalis. These FDHs detoxify formate and we show that their expression provides C. albicans with a growth advantage in the presence of formate. 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.