Antibiotics Change Gut Bacteria Balance

By Richard Asa @RickAsa
October 03, 2016

Even one round may be changing the makeup of the gut.

Several studies have shown that taking antibiotics can change the composition of your intestinal microflora, killing off some beneficial bacteria. 


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In one study at Stanford University, researchers found that repeated use of an antibiotic caused “cumulative and persistent changes in the composition of the beneficial microbial species inhabiting the human gut.” 

Another study at the University of California-Davis found that antibiotics deplete good bacteria in the gut, including those that breakdown fiber from vegetables, which create an energy source to absorb water and oxygen. 

“Unlike Clostridia and other beneficial microbes in the gut, which grow anaerobically, or in the complete absence of oxygen, Salmonella flourished in the newly created oxygen-rich micro environment after antibiotic treatment,” said Andreas Bäumler, PhD, professor of medical immunology and microbiology at UC Davis Health System said. “In essence, antibiotics enabled pathogens (bad bacteria) in the gut to breathe.” 

A third study showed that a single course of antibiotics “has enough strength to disrupt the normal makeup of microorganisms in the gut for as long as a year,” potentially leading to antibiotic resistance. Researchers said that antibiotics attack good bacteria in the gut as well, sometimes causing long-term changes that favor bad bacteria that can lead to disease.

“Clearly,” the study says, “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.”

Colonies of microflora in the gut provide many benefits, including contributing to the host’s nutrition and protecting the host from infection. In most cases of antibiotic use, the bacterial populations in some colonies are reduced in numbers while those in other colonies increase. In some cases, the increased numbers of certain bacteria give rise to resistant strains of bacteria or overgrowth by fungi, the study says. 


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It’s even been found that taking antibiotics at an early age can contribute to obesity later in life, according to National Geographic

“I’m not saying people should never take antibiotics,” says Martin Blaser, MD, from the NYU Langone Medical Center, who led the study. “But we need to be more judicious. Antibiotics can have long-term consequences. I hope that knowledge will enter the examining room, so that parents don’t demand antibiotics and doctors are more cautious about using them.”

It became clear, after exhaustive tests with penicillin in mice, that antibiotics change the gut microbes and the mice’s metabolism. The medication increased inflammation and the risk of obesity. 

Mice aren’t humans, but a few studies that tracked the health of human babies over time “found that early antibiotic exposure does affect body weight at later ages.”. A 2014 study found that 32 percent of children who received antibiotics before their first birthday were overweight at age 12, compared to just 18 percent of those who didn’t.

Blaser had earlier commented, in Nature, that sometimes the “friendly flora never recover. These long-term changes to the beneficial bacteria within people’s bodies may even increase our susceptibility to infections and disease. Overuse of antibiotics could be fuelling the dramatic increase in conditions such as obesity, type 1 diabetes, inflammatory bowel disease, allergies and asthma, which have more than doubled in many populations.”

It’s a given that antibiotics are already overprescribed in adults and children and that controlling overprescribing is a difficult challenge in the fight to control superbugs in the gut. But an increasingly better understanding of the microflora in the gut could change perception enough to reduce antibiotic overuse, says Blaser. 


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March 26, 2020

Reviewed By:  

Christopher Nystuen, MD, MBA