A new study from the University of Chicago, published in Nature, shows that the typical Western-style diet—rich in processed foods, red meat, dairy products, and sugary treats—can make it harder for the gut to recover after taking antibiotics.
This diet, which is low in fruits, vegetables, and whole grains, not only reduces the diversity of healthy gut bacteria but also weakens the body’s ability to bounce back after antibiotic treatments.
The research, led by Megan Kennedy, a student in the Medical Scientist Training Program, found that mice fed a Western-style diet struggled to restore a healthy balance of gut bacteria after antibiotics, leaving them vulnerable to infections like Salmonella.
The researchers also studied mice that were given a diet resembling the Mediterranean style, which is high in plant-based fiber from fruits, vegetables, and whole grains.
These mice were able to recover a healthy and diverse microbiome much faster after antibiotic treatment compared to those on the Western diet. This difference amazed the researchers, as it showed how dramatically food choices can impact gut health and recovery.
Antibiotics are known to disrupt the gut microbiome, wiping out not only harmful bacteria but also many of the good ones that help maintain a healthy digestive system. Eugene B. Chang, MD, a senior author of the study and a professor of medicine at UChicago, compared the gut microbiome’s recovery to that of a forest after a fire.
He explained that, just like a forest, the gut needs specific nutrients at specific times to rebuild its community of microbes properly. The Western diet, which is heavy on processed foods and low in fiber, does not provide the right nutrients for this process. Instead of a balanced recovery, only a few types of bacteria take over, preventing the full restoration of a healthy gut ecosystem.
Dr. Chang’s comparison to a forest recovery is not just poetic; it’s scientifically grounded. Chang’s colleague, Joy Bergelson, Ph.D., who studies plant and microbe interactions, further supported this view. Just like forests require certain conditions to regrow properly, the gut also needs the right kind of food—like fiber-rich plants—to recover its balance of good bacteria.
In their experiments, the team fed one group of mice a Western-style diet and another group regular mouse chow that had more plant fiber and less fat. Both groups were given antibiotics to disrupt their gut bacteria.
Afterward, some mice remained on their original diet, while others were switched to the opposite one. To see if they could speed up recovery, the researchers also tried fecal microbial transplants (FMT), where gut bacteria from healthy mice were transferred to the antibiotic-treated mice.
The results were clear. Mice that ate a fiber-rich diet, either before or after antibiotics, were able to restore their healthy gut bacteria much more effectively than those on the Western diet. Even when FMT was used, it didn’t help the Western diet mice recover.
This was a surprising discovery since FMT is often considered a reliable way to restore gut health. According to Kennedy, it didn’t seem to matter how ideal the microbial transplant was—the Western diet prevented the good bacteria from re-establishing themselves properly.
Another troubling finding was that the mice on the Western diet were more likely to get infections from Salmonella. This suggests that their weakened gut microbiomes left them less able to fight off harmful pathogens. This is particularly concerning since both antibiotic overuse and unhealthy diets are common in many parts of the world, including the United States.
The research points to a powerful link between diet and gut health. Kennedy and Chang suggest that diet could even be used as a medical tool to help patients recover from strong antibiotic treatments.
For example, cancer patients or organ transplant recipients are often given powerful antibiotics and immunosuppressant drugs, which can leave them vulnerable to infections. Instead of just adding more antibiotics, which could make things worse, changing the patient’s diet to include more fiber-rich foods could help rebuild their gut health naturally.
Chang also mentioned that he is working on developing dietary supplements that could boost gut health even if people do not make big changes to their eating habits. He believes that food could become a type of medicine, helping people recover faster and avoid infections simply by adjusting what they eat.
This study serves as a strong reminder that what we eat directly affects our health, not just in obvious ways like weight and energy levels but deep inside our bodies, where our gut bacteria live. A diet filled with fruits, vegetables, and whole grains can help maintain a healthy microbiome that can recover more easily after disruptions like antibiotics.
Meanwhile, a Western-style diet can make recovery much harder, leaving the body exposed to harmful infections. For those facing surgery or strong medical treatments, adding more healthy foods to their diet could be a simple yet powerful way to protect their health.
As Chang summed it up, “I’ve become a believer that food can be medicinal. In fact, I think that food can be prescriptive because we can ultimately decide what food components are affecting which populations and functions of the gut microbiome.”
For more information about gut health, please see recent studies about the crucial link between diet, gut health, and the immune system and results showing that Low-gluten, high-fiber diets boost gut health and weight loss.
For more information about gut health, please see recent studies about Navigating inflammatory bowel disease (IBD) with diet and results showing that Mycoprotein in diet may reduce risk of bowel cancer and improve gut health.
The research findings can be found in Nature.
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