The foods we eat influence more than just energy levels and weight—they shape the microbial communities in our digestive system, which play a crucial role in overall health. A typical Western-style diet, heavy in processed foods, red meat, dairy, and sugar but lacking in fiber-rich fruits, vegetables, and whole grains, has been shown to reduce gut microbial diversity. This depletion is linked to immune-related conditions such as inflammatory bowel disease.
A new study in Nature from University of Chicago researchers explores how diet affects the gut microbiome’s ability to recover after antibiotic treatment. The findings suggest that mice fed a Western-style diet struggled to rebuild a healthy, diverse microbiome following antibiotics, leaving them more vulnerable to pathogens like Salmonella. However, mice on a diet rich in plant-based fiber—similar to the Mediterranean diet—experienced faster recovery and greater resilience.
Antibiotics and the Gut: A "Forest Fire" Effect
While antibiotics effectively combat harmful bacteria, they also wipe out beneficial microbes that help maintain a balanced gut ecosystem.
“The mammalian gut microbiome is like a forest, and when you damage it, it must have a succession of events that occur in a specific order to restore itself back to its former health,” explained Eugene B. Chang, MD, a senior author of the study and professor of medicine at the University of Chicago. “When you are on a Western diet, this does not happen because it doesn't provide the nutrients for the right microbes at the right time to recover. Instead, you end up with a few species that monopolize these resources, and don’t set the stage for other organisms that are required for recovery.”
Led by Megan Kennedy, a student in the Medical Scientist Training Program at UChicago, the research investigated how diet influences microbiome recovery in mice following antibiotic exposure. The team found that only mice consuming a fiber-rich diet—either before or after antibiotics—were able to restore a balanced gut microbiome.
Importantly, fecal microbial transplants (FMT), a method of introducing healthy gut microbes from one individual to another, did not significantly aid recovery for mice on a Western-style diet. Without the necessary nutrients, transplanted microbes struggled to establish themselves in the gut.
“It doesn’t seem to matter what microbes you’re putting into the community through FMT, even if it’s matched in every way possible to the ideal transplant,” Kennedy said. “If the mice are on the wrong diet, the microbes don’t stick, the community doesn’t diversify, and it doesn’t recover.”
The Future of Diet as Medicine
Beyond general health benefits, this study highlights how diet could play a key role in clinical treatments, particularly for patients recovering from antibiotic use. Individuals undergoing cancer treatment or organ transplants are often given powerful antibiotics and immunosuppressants, increasing their risk of multidrug-resistant infections.
“Maybe we can use diet to rebuild the commensal microbes that have been suppressed under these therapies,” said Chang. “We can restore the healthy microbiome much quicker and prevent the emergence of more multidrug-resistant organisms.”
Though shifting to a plant-based diet overnight isn’t realistic for everyone, small dietary adjustments could help improve gut health. Kennedy suggests increasing fiber intake before anticipated antibiotic treatments, such as before surgery, to promote microbiome resilience. Meanwhile, Chang is exploring supplement-based solutions to strengthen gut health without requiring major dietary overhauls.
“I've become a believer that food can be medicinal,” Chang said. “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.”
The study, Diet outperforms microbial transplant to drive microbiome recovery in mice, was supported by funding from the National Institutes of Health, the Gastrointestinal Research Foundation of Chicago, the Simons Foundation, and additional collaborators.