What Happens to the Gut Microbiome After Taking Antibiotics?

Studies are finding that a single course of antibiotics alters the gut microbiomes of healthy volunteers—and that it can take months or even years to recover the original species composition.

Written bySophie Fessl, PhD
| 5 min read
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The development of antibiotics was a breakthrough in medicine. But while they can save lives, they have a dark side. Microbes resistant to the drugs were responsible for more than one million deaths in 2019, according to a study published earlier this year in The Lancet.

Furthermore, a growing number of studies are finding that even a short course of antibiotics can alter the makeup of the bacterial species in the gut. These community changes can be profound, with some people’s microbiomes taxonomically resembling those of critically ill ICU patients after taking the drugs. And the microbes that survive the treatment tend to carry resistance genes, potentially enabling pathogens to acquire the means to evade our best pharmacological weapons.

Overall, Washington University School of Medicine in St. Louis pathologist and microbiologist Gautam Dantas says that the findings are a warning that “taking antimicrobials is a gamble every single time you ...

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Meet the Author

  • Headshot of Sophie Fessl

    Sophie Fessl is a freelance science journalist. She has a PhD in developmental neurobiology from King’s College London and a degree in biology from the University of Oxford. After completing her PhD, she swapped her favorite neuroscience model, the fruit fly, for pen and paper.

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