Abstract: The present invention provides method of making a protein hydrolysate formula and protein hydrolysate formulas made thereby for downregulating hypersensitivity and for promoting gut immune barrier, and methods of preventing or treating allergies, especially cow's milk allergy by combining the protein with probiotic gastrointestinal bacteria, especially Lactobacilli. The probiotics make it possible to influence the immunological balance, whereby allergy can be prevented by affecting the initiation mechanism of allergy. The present invention makes it possible to develop a person's tolerance of proteins by actively promoting a tolerogenic immune response. In addition, present invention provides for administering fragments of an allergen modified by probiotic gastrointestinal bacteria in order to desensitize a immune response to systemic hyporesponsiveness.