A method and system for targeting the microbiome to promote health involves exposing an expectant mother to a mixture of farm derived manure-containing soil to reduce the chances her baby will suffer allergies and autoimmune diseases. City dwelling expectant mothers are exposed to immunologic agents and allergens in a fashion (e.g., via exposure to farm animal manure-containing soils) that charges their immune system and that of their fetus(es) so that their babies, once born, are provided with immunity against a variety of autoimmune diseases, including allergies commonly and increasingly experienced in modern urban environments.