Antibiotics Delete Gut Diversity

Study finds that even a single course of antibiotics can cause long-lasting damage to microbiome
December 17, 2018 Updated: December 17, 2018

It can take six months to regain a normal microbiome—the essential bacteria that live in our stomach—after using antibiotics, and chances are good that not all of the microbes present before the antibiotics were administered will return.

Researchers in Copenhagen conducted a small study (12 men) that examined gut diversity after a single course of antibiotics. They used three drugs considered antibiotics of last resort: meropenem, gentamicin, and vancomycin.

While the gut microbes of the subjects recovered, nine common species of gut bacteria could no longer be detected in their microbiome.

“In this case, it is good that we can regenerate our gut microbiota which is important for our general health. … The concern, however, relates to the potentially permanent loss of beneficial bacteria after multiple exposures to antibiotics during our lifetime,” said Oluf Pedersen, the lead scientist of the study.

Only One

This is what happens after a single course of antibiotics. But what happens in the United States, where outpatient health care providers prescribed more than 266 million courses of antibiotics in 2014, a third of which the Centers for Disease Control says are unnecessary?

The same year saw an average of 835 antibiotic prescriptions for every 1,000 people. People who suffer from recurrent urinary tract infections or chronic respiratory infections are likely to be given multiple courses of antibiotics in a single year. If it takes six months to mostly recover from a single course of antibiotics, those who take multiple courses are losing their chance to have a healthy, balanced microbiome.

It’s common to see articles comparing the gut bacteria of indigenous tribes with that of your average American. The indigenous microbiome is always more diverse. M. Gloria Dominguez-Bello is a microbiologist at the New York University School of Medicine and one of the authors of a study of the Yanomami tribe, first visited by the modern world in 2009.

While Dominguez-Bello mentions diet, she also notes the difference in antibiotic use. The 2009 visit to the Yanomami in the Amazon is the first time the tribe was exposed to antibiotics, which can have a serious effect on gut health.

“Antibiotics kill bacteria in the gut, and sometimes species don’t come back. … This is especially true with children, whose microbiomes are in the process of getting assembled. Impacts on the microbiome at a young age can have long-lasting consequences,” Domingues-Bello told NPR.

More and Different and Better

Is it possible to replenish your gut bacteria after a course of antibiotics? The answer is both yes and no. You can bring your microbes back, but they will no longer be the same. Each time the microbiome is mowed down and resurrected, diversity and the immune system’s ability to adapt are reduced. Combine that news with the rise of antibiotic-resistant bacteria and you should want to be as far away from antibiotics as possible. It pays to take a look at the other likely reason for indigenous peoples microbiome diversity: diet.

Kristina Martin is a writer for, which originally published this article.