The invention features the treatment of gastrointestinal disorders associated with an innate immune response tiggered by alpha amylase inhibitor CM3, alpha amylase inhibitor 0.19 (0.19), CM1, CM2, CMa, CMd, CM16, CMb, CMX1/CMX3, CMX2, and/or alpha amylase inhibitor 0.53 (0.53). To this end, the invention features pharmaceutical compositions including neutralizing antibodies to CM3, 0.19, CM1, CM2, CMa, CMd, CM16, CMb, CMX1/CMX3, CMX2, and/or 0.53, food products containing reduced levels of CM3, 0.19, CM1, CM2, CMa, CMd, CM16, CMb, CMX1/CMX3, CMX2, and/or 0.53 protein, the use of oral TLR4 inhibitors to block the effect of said alpha-amylase inhibitors, assays for identifying CM3, 0.19, CM1, CM2, CMa, CMd, CM16, CMb, CMX1/CMX3, CMX2, and/or 0.53 content in food products, and assays for diagnosing subjects with a disorder related to CM3, 0.19, CM1, CM2, CMa, CMd, CM16, CMb, CMX1/CMX3, CMX2, and/or 0.53 triggered innate immune responses.
