As someone who grew up on a dairy farm, who worked on a farm, and who has friends and family operating their own farms, I'd like to point out that this is backwards. Farmers know that bacteria can make them sick or even kill them. It's the city-slickers who have never been truly ill who think that they're harmless.

Auto-immune diseases and allergies are nowhere even slightly near as big a problem as dysentery and other food borne illnesses used to be. There are far more people who died of TB from contaminated milk alone than people dieing of allergies.

It's true that other aspects of improved care have also reduced the risk from food borne illnesses - antibiotics, clean water, IV rehydration and others.

Current, modern day humans live longer, healthier lives than any who have ever lived before.