Research has offered compelling evidence that taking antibiotics changes the composition of microbes in the guts of humans and animals.

Studies have also shown that imbalances in gut bacteria lead to adulthood diseases.

What’s been missing is the link in the middle — the science demonstrating that antibiotic usage causes the changes in the digestive system that then lead to higher risks of adult diseases.

“That requires a longitudinal study with a large number of children all taking the same antibiotics, and the analysis gets complicated very quickly,” said Dan Knights, a computational biologist at the University of Minnesota.

So Knights and colleagues did one of the next best things — pooling the data from existing studies on both ends of the issue and analyzing it together. What they found, according to an article published last week in the scientific journal Cell Host & Microbe, is some of the strongest evidence yet that antibiotic usage is at least associated with changes in the gut that increase the risk of certain infectious diseases, allergies, autoimmune disorders and even obesity later in life.

“Diseases related to metabolism and the immune system are increasing dramatically, and in many cases we don’t know why,” Knights said.

The researchers also developed a stool sample test that could one day be used to monitor changes in gut bacteria in children, which could indicate risks for future conditions.

Cause and effect is far, far from being proven, but Knights said the findings at least add to the body of research that discourages overuse of antibiotics or “just in case” prescriptions for worried patients. However, he stressed that antibiotics are “lifesaving” treatments for bacterial infections that should be taken when appropriate.

“You might have a discussion with your doctor[s] about whether they think they are necessary,” he said, “and whether they know if this is a bacterial infection vs. a viral infection.”