• Increased antibodies against microbial antigens were detected in both Crohn's disease patients and animal models of gut inflammation. The Cbir1 epitope of bacterial flagellin protein was immunodominant in both settings• CBir1 TCR transgenic mice have CD4+ T cells capable of recognizing bacterial flagellin and other commensal microbes• Activation of adoptively transferred naïve Cbir1 TCR cells does not occur under steady-state conditions but can be achieved via disturbance of the intestinal mucosal barrier or lack of immunoregulatory mechanisms. This evidence concerns the gene CD4 and Crohn disease.