We found upregulation of genes associated with cytokine responses previously shown to be important in C. difficile pathogenesis, including IL23A, which is associated with increased colonic inflammation and mortality in animal models of CDI [13, 29, 30], and IL34, which is upregulated in tissues of patients with inflammatory bowel disease and in mouse models of experimental colitis [31, –33]. Here, IL23A is linked to inflammatory bowel disease.