Bugs in the gut may be causing many allergy symptoms felt in the head, from runny noses to trouble breathing, researchers said. And antibiotics could be to blame, the researchers told a meeting of the American Society for Microbiology.

The findings could help explain the puzzling rise in asthma and allergies across the developed world in recent decades, the University of Michigan researchers said. Antibiotics kill bacteria, but they can kill beneficial bacteria living in the intestines and colon.

Many doctors recommend that patients taking antibiotics also eat “live” yogurt to replace some of these helpful microbes. “We all have a unique microbial fingerprint a specific mix of bacteria and fungi living in our stomach and intestines,” said Dr. Gary Huffnagle, an associate professor of internal medicine and of microbiology and immunology at the University of Michigan.

“Antibiotics knock out bacteria in the gut, allowing fungi to take over temporarily until the bacteria grow back after the antibiotics are stopped. Our research indicates that altering intestinal microflora this way can lead to changes in the entire immune system, which may produce symptoms elsewhere in the body.”

Experiments on mice suggest that altering the balance of these so-called intestinal flora can affect the immune system.

“After antibiotics changed the mix of microbes in the gastrointestinal tract, the mice developed an allergic response in the lungs when exposed to common mold spores,” Huffnagle said in a statement. “Mice that didn’t receive the antibiotics were able to fight off the mold spores.”

Huffnagle told the meeting that if the findings also hold true in people, they could help explain why asthma and allergies are on the rise. “Anything you inhale, you also swallow,” Huffnagle said in a statement. “So the immune cells in your GI (gastrointestinal) tract are exposed directly to airborne allergens and particulates.

This triggers a response from immune cells in the GI tract to generate regulatory T-cells, which then travel through the bloodstream searching the body for these antigens.” The immune system cells then block the development of allergic responses.

When antibiotics wipe out the bacterial population in the GI tract, yeast and fungi move in and multiply.

Fungi may secrete compounds called oxylipins, which can control the type and intensity of immune responses, Huffnagle told the meeting, being held in New Orleans.

Having too many oxylipins may prevent the development of the regulatory T-cells, in turn allowing for a hyperactive immune response against allergens such as pollen, he proposed.