The invention relates to microorganisms for the treatment of food allergies, specifically coeliac disease, as well as to methods for the selection thereof. The action mechanisms of said microorganisms include: (i) the regulation of the innate and adaptive immunological responses; (ii) the reduction of the concentration of toxic gluten peptide epitopes in the intestinal lumen; (iii) the strengthening of the barrier defence function against harmful antigens and bacteria; and (iv) the provision of enzymatic activities that promote digestion.