Taking Antibiotics Can Change the Gut Microbiome for Up to a Year

A new study illuminates the problems antibiotic overuse could cause for individual patients.

Tobias Schwarz / Reuters

Doctors and patients alike should be thoughtful about starting antibiotics—not only because of the well-publicized resistant bacteria that are proliferating thanks to overuse of those drugs, but also because, a new study illustrates, there could be serious consequences for the individual. As well as for, you know, humanity in general.

The study, recently published in mBio, found that just one weeklong course of antibiotics changed participants' gut microbiomes, with the effects sometimes lasting as long as a year. After all, antibiotics don’t discriminate—as they attack the bad bacteria, the good ones are vulnerable too.

In a randomized, placebo-controlled clinical trial at two centers (one in the United Kingdom, one in Sweden), researchers gave participants one of four commonly-prescribed antibiotics—clindamycin, ciprofloxacin, minocycline, and amoxicillin—or a placebo. They checked on participants’ oral and gut microbiomes by analyzing the bacteria present in their saliva and feces before the experiment (to get a baseline), right after the week of antibiotics, and one, two, four, and 12 months afterward.

The effects varied depending on which antibiotic the person took, but generally, while the oral microbiome bounced back pretty quickly, some of the bacteria in the intestines suffered a crushing blow. People who took clindamycin and ciprofloxacin saw a decrease in types of bacteria that produce butyrate, a fatty acid that lowers oxidative stress and inflammation in the intestines. The reduced microbiome diversity for clindamycin-takers lasted up to four months; for some who took ciprofloxacin, it was still going on at the 12-month check-up. (Amoxicillin, on the plus side, seemed to have no significant effect on either the oral or gut microbiome, and minocycline-takers were back to normal at the one-month check-up.)

What’s more, the researchers found that while “both study populations carried antibiotic-resistance genes in their oral and gut microbiomes” before the study began, genetic analyses revealed the presence of more of these genes after people had taken the antibiotics.

“Clearly,” the study reads, “even a single antibiotic treatment in healthy individuals contributes to the risk of resistance development and leads to long-lasting detrimental shifts in the gut microbiome.”