Just One Antibiotic Treatment Can Alter Your Gut Microbiome For A Year

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Janet Fang 13 Nov 2015, 21:43

The same antibiotic treatment can elicit very different responses from your mouth microbes and from your gut microbes. While the microscopic communities living in your mouth rebound quickly, just one course of antibiotics can disrupt the gut microbiome for months, sometimes even up to a year, according to findings published in mBio this week. 

Because of “superbugs” and the spread of resistance, lots of research is going into the effects of – and possible collateral damage caused by – antibiotic exposure. But the focus has been mostly on microbial communities residing in the gut. Ecological consequences for the different niches of individual microbiomes have been largely ignored. 

In two randomized, placebo-controlled clinical trials, a team led by University of Amsterdam’s Egija Zaura followed the oral and gut microbiomes of 66 healthy adults living in the U.K. and Sweden. Each participant was given either a placebo or one of four common oral antibiotics: clindamycin, ciprofloxacin, amoxicillin, and minocycline. The researchers collected their saliva and feces before, immediately after, and one, two, four, and 12 months the antibiotics or placebo were administered. Genes from a total of 391 saliva and 389 fecal samples were sequenced. 

The salivary microbiome was far more robust, they found, bouncing back in as little as a week. It’s possible that oral microbial ecosystems possess a higher intrinsic resilience toward stress. After all, our mouths endure multiple daily perturbations thanks to oral hygiene: exposure to topical antimicrobial agents (such as toothpaste and mouthwash) and tooth brushing itself, as well as constant changes in temperature and oxygen. 

That’s not the case for the colon. So while their salivary microbiome composition remained unexpectedly stable, their fecal microbiome was severely and negatively impacted in the long term. Diversity was significantly reduced for up to four months in the clindamycin group – and even up to 12 months in the ciprofloxacin group. In particular, helpful microbial species that produce a short-chain fatty acid called butyrate became strongly underrepresented (butyrates are important for cells that line our colon). Furthermore, exposure to antibiotics enriched genes that have previously been implicated in antibiotic resistance. Taking out the helpful microbes in a healthy person’s gut clears the way for germs and other pathogens to wreak havoc. 

But here’s the flip side: Understanding the mechanisms behind the resilience of the oral microbiome could help us better combat microbial imbalances elsewhere in the body.

[H/T: Ars Technica]

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