The rates of allergies and asthma have skyrocketed in the past 40 years, for reasons that have been frustratingly unclear. Now it turns out that the rise of another phenomenon—the use of antibiotics—may hold a clue. A study from the University of Michigan Medical School has found that antibiotics seem to prime the immune system to overreact to substances it could just as well ignore.

When the Michigan team gave mice a five-day course of antibiotics, the animals showed the same effect seen in humans: an upset in the balance of yeast and other microbes in the gut. The researchers then exposed the mice to several common allergens. The mice given antibiotics were hypersensitive to them, while the other mice had a normal immune response.

While we tend to think of allergies and asthma as involving mainly the respiratory system, this research suggests the microbes in the gut play a role, too.

The results support part of the “hygiene hypothesis,” which holds that modern societies are too sanitary—when you’re not exposed to very many bugs, your immune system has a hard time telling the difference between a harmless substance (like pollen) and a dangerous toxin, so it’s likely to overreact.

And the findings provide yet another reason to encourage the growth of “good” bacteria in our bellies. To do that, Gary Huffnagle, who worked on the study, recommends a diet rich in fiber and active-cultured yogurt and low in refined carbs and sugar. “It’s a good idea to do this even when you’re not taking antibiotics,” he says. And if you do need to take the drugs, he advises taking probiotics afterward. Your nose, as well as your stomach, will thank you.