Shared metabolism between a bacterial and fungal species that reside in the human gut.

Abstract

The fungal species <i>Candida albicans</i> and the bacterium <i>Enterococcus faecalis</i> are members of the human gut microbiome. To explore the range of interactions between these two species, we utilized dual RNA-sequencing to transcriptionally profile both <i>C. albicans</i> and <i>E. faecalis</i> during coculture (compared with monoculture controls) under two conditions: 1) an in vitro setting that mimics certain features of the gut environment and 2) a gnotobiotic mouse gut model. RNA-seq analysis revealed a large number of gene expression changes induced by one species in the presence of the other. More specifically, both species highly upregulate citrate-metabolizing genes during coculture: <i>C. albicans</i> upregulates <i>CIT1</i> (citrate synthase) which produces citrate, while <i>E. faecalis</i> upregulates its <i>cit</i> operon, which breaks down citrate. In vitro analysis showed directly that citrate cross-feeding (production of citrate by <i>C. albicans</i> and breakdown by <i>E. faecalis)</i> enhances growth of <i>E. faecalis</i>. A main byproduct of citrate metabolism in <i>E. faecalis</i> is formate, a short chain fatty acid toxic to fungi. Our RNA profiling revealed that <i>C. albicans</i> upregulates three formate dehydrogenases (FDHs) during coculture; we show that the FDH genes confer a growth advantage to <i>C. albicans</i> when <i>E. faecalis</i> (or simply formate) is present. These findings reveal a metabolically driven cycle between <i>C. albicans</i> and <i>E. faecalis</i> in the mouse gut and in vitro, where cross-feeding of citrate and detoxification of formate facilitates the growth of both species when they are cultured together.