Microbial interactions impact the growth response of Clostridioides difficile to antibiotics

In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.