A new study suggests that the immune system’s reaction to antibiotics could make people more prone to allergies.

Scientists found that antibiotics changed microbes in the gastrointestinal tracts of mice, affecting how the immune system responds to common allergens in the lungs.

“We all have a unique microbial fingerprint - a specific mix of bacteria and fungi living in our stomach and intestines,” said Gary Huffnagle, an associate professor of internal medicine and of microbiology and immunology at the University of Michigan Medical School. “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,” he said.

In the study, researchers gave mice a five-day course of oral antibiotics. Two days after stopping the antibiotics, the mice were exposed to a common mold allergen.

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

If the findings are confirmed in human clinical studies, Huffnagle believes they could help explain why cases of chronic inflammatory diseases - like asthma and allergies - have been increasing rapidly over the last 40 years, a time period that corresponds with widespread use of antibiotics.

Researchers explained that the relationship between the gastrointestinal, respiratory and immune systems in the human body is important in this study because bits of pollen, dust and spores are trapped throughout the body before reaching the lungs. The trapped particles are swept into the stomach with saliva and mucus as people swallow.

“Anything you inhale, you also swallow,” Huffnagle explained. “So the immune cells in your GI tract are exposed directly to airborne allergens and particulates.”

Huffnagle said that when antibiotics reduce the bacterial population in the GI tract, the number of yeast and other fungal organisms increases.