An improved method of detoxifying gluten proteins from cereal grains produces detoxified cereal grains with a reduction of antigenicity of toxic epitopes of gluten proteins by up to a range between 0 and 20 ppm. The detoxified cereal grains can be advantageously used for preparation of of food products (e.g. bakery products, pasta or dairy products) having a manifest preventive and/or therapeutic effect for gut dysbiosis caused by bacterial or viral infective agents or by pathologies with a strong inflammatory or autoimmune component such as celiac disease, ulcerative colitis, Crohn's disease and irritable intestine syndrome.