Clostridioides difficile couples responses to host nutritional immunity and a commensal-derived antibiotic to enable growth in the gut.

The Gram-positive opportunistic pathogen Clostridioides difficile colonizes the gut by adapting to an array of threats from the host and the microbiome. A potential threat from the microbiome is the antimicrobial peptide bacitracin, which is produced by the commensal Bacillus licheniformis and prevents dephosphorylation and recycling of undecaprenyl phosphate, a lipid carrier essential in cell wall biogenesis. Gram-positive bacteria typically use multiprotein membrane complexes called Bce modules to sense and respond to bacitracin. We identified a Bce module in C. difficile that incorporates the undecaprenyl pyrophosphatase BacA2 into the bacterium's response to bacitracin. This Bce module was essential for C. difficile survival in the presence of B. licheniformis or bacitracin in vitro and in mice. Expression of the genes encoding the Bce module was inhibited by Fur, a transcriptional repressor that controls the expression of genes critical for responding to host-mediated restriction of iron availability in the gut. Low iron reduced undecaprenyl phosphate biosynthesis and sensitized C. difficile to bacitracin. Our findings support a model in which C. difficile is affected independently and collectively by low iron and bacitracin, leading to the inhibition of undecaprenyl phosphate recycling. In response, C. difficile increases the transcription of undecaprenyl recycling and bacitracin efflux genes that are controlled both by Fur and a Bce module. This distinct Bce module forms a system that responds to nutritional immunity and antimicrobial molecules produced by microbiome members to maintain envelope integrity and support host colonization.