What you need to know about the effects of antibiotics on the gut microbiome

The educational content in this post, elaborated in collaboration with Lesaffre, was independently developed and approved by the GMFH publishing team and editorial board.

Antibiotics may cause an irreversible depletion of gut bacteria

Since 2000, global antibiotic use has increased by 66% and continues to rise at a rapid pace¹. While antibiotics are a cornerstone of modern medicine, saving countless lives each year, they can also disrupt the delicate balance of the gut ecosystem. The gut bacteria most impacted by antibiotics include the Bacteroidetes, Firmicutes, and Actinobacteria taxa. These groups play crucial roles in the gut microbiome, such as metabolizing dietary fiber and polyphenols, synthesizing vitamins, regulating the immune system, maintaining gut barrier integrity, and protecting against enteric pathogens².

The loss of gut microbiome diversity directly leads to the formation of a new ecosystem where beneficial bacteria may be unable to control Clostridioides difficile and other pathogenic bacteria that naturally reside in the gut, such as C. perfringens, Staphylococcus aureus, and Klebsiella oxytoca. These pathogens can overgrow when the gut microbiota that keeps them under control is wiped out^2,3.

Beyond the loss of protective bacteria, the overuse of antibiotics—particularly when they are not the appropriate treatment—is a key factor in the development of antibiotic-resistant pathogens. This occurs through the natural selection of bacteria that that are more resistant to the drugs. As a result, there is an overgrowth of antibiotic-resistant bacteria, some of which are capable of degrading antibiotics within the gut, which in turn shields other pathogens from the antibiotics’ effects, ultimately leading to a decline in their effectiveness⁴. Yet, other resistance mechanisms apply as well. The proliferation of drug-resistant microbes is responsible for more than one million deaths and is recognized by the Centers for Disease Control and Prevention as a major threat to public health⁵.

Exposure to antibiotics can have long-term health consequences

Exposure to antibiotics in infancy is associated with an increased lifetime risk of infections, asthma, obesity, inflammatory bowel disease, and neurodevelopmental disorders. These effects are largely due to antibiotics’ ability to disrupt the gut microbiome, leading to increased intestinal permeability and inflammation, reduced levels of short-chain fatty acids, and altered immune cell development⁶.

Antibiotics can have long-lasting effects on adults’ gut microbiomes. Recent studies involving healthy adults found that gut microbiome diversity was impacted as early as one day after the treatment ended and remained altered for up to six months^7,8. The gut microbiome of these healthy participants taking antibiotics temporarily resembled that of a patient in the intensive care unit⁹. In addition, the gut microbiome of some people taking antibiotics may serve as a reservoir for resistance genes that could be passed on to others¹⁰. Antibiotics may cause the gut microbiome to shift to an alternative stable state, the full implications of which are only now becoming clearer^10-12.

How can you mitigate the side effects of antibiotics? Here’s what the latest science suggests

The side effects of antibiotics—such as diarrhea, gas, cramping, and nausea—are often due to a reduction in the microbial richness and diversity of the gut microbiome. To maintain or restore the gut microbiome after antibiotic use, current strategies include community replacement with probiotics or the administration of prebiotics³.

The best available scientific evidence suggests that some probiotics may have a moderate effect for preventing antibiotic-associated diarrhea in children, adults, and elderly adults¹³. This is explained by the capacity of probiotics to stimulate short-chain fatty acids production, protect the resident gut microbiome and gut barrier integrity, and protect against local inflammation¹⁴. However, this benefit is strain-specific, meaning that not all probiotics show efficacy for antibiotic-associated diarrhea^13,14.

Not all probiotics are effective for recovering gut health after antibiotic use¹⁵. However, two well-researched probiotics, the yeast Saccharomyces boulardii CNCM I-745 and the bacterium Lacticaseibacillus rhamnosus GG, have shown promise, particularly in children and adults at risk of antibiotic-associated diarrhea^13,14. Yeast probiotics offer advantages over bacterial probiotics, including better survival in the harsh conditions of the stomach, which allows them to reach the small and large intestines in an active state, and they can continue to be effective when administered alongside antibiotics¹⁶.

To maximize the benefits of probiotics, they should be introduced at the start of antibiotic treatment, with higher doses generally proving more effective than lower ones. In most clinical trials, probiotics were administered for the duration of antibiotic treatment and an additional seven days afterward. However, the best duration of probiotics after the cessation of antibiotics that allows the recovery of the gut ecosystem is unknown¹⁷.

A low-fiber diet may exacerbate the impact of antibiotics on the gut microbiome, delaying recovery, which suggests that prebiotic fibers are also important for the recovery of the gut microbiome after antibiotic use¹⁸. Prebiotics such as mucin glycans and xanthan gum may promote the growth of beneficial gut microorganisms of the microbiome, prevent the colonization of pathogenic bacteria, and boost the production of short-chain fatty acids in the gut following antibiotics³. After completing an antibiotic course, consuming foods rich in fermentable fiber may help restore healthy gut bacteria and is associated with reduced antibiotic resistance¹⁹.

Other potential tools for restoring gut health post-antibiotics, though not yet widely available, include fecal microbiota transfers. Administering a fecal microbiota transfer from the same individual could lead to faster microbiome restoration²⁰, as could the use of defined communities of microorganisms, such as live purified or synthetic microbial consortia³. Scientists are also exploring using non-antibiotic drugs alongside antibiotics to enhance their effectiveness without harming beneficial gut bacteria²¹. Additional strategies to mitigate the consequences of antibiotic use include reducing gut antibiotic levels through enzymatic degradation or sequestration, which helps minimize broader negative impacts on the composition and function of the gut microbiome³.

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