Why your gut can’t heal on a Western diet

The gut takes a direct hit from the Western-style diet, which is heavy on processed foods, red meat, dairy, and sugar – and low on fruits, vegetables, and whole grains.

This way of eating reduces the variety of microbes living in the digestive system, weakening the gut’s resilience. That microbial decline can interfere with how the body responds to antibiotics and makes it harder for the immune system to fight off disease.

In a new study from the University of Chicago, scientists show how mice fed a Western-style diet were unable to restore a healthy gut microbiome after antibiotic treatment. Not only did these mice struggle to regain microbial diversity, but they also became more vulnerable to infections like Salmonella.

On the other hand, mice that ate a diet resembling the Mediterranean pattern – rich in plant-based fiber from fruits, vegetables, and whole grains – bounced back quickly after antibiotic exposure.

“We were really surprised by how dramatically different the recovery process is in the mice on the Western-style diet versus the healthier one,” said study lead author Megan Kennedy.

A gut that can’t regrow

Antibiotics are designed to wipe out harmful bacteria, but they don’t stop there. They often destroy helpful gut bacteria as well. This mass destruction is what scientists compare to a forest fire. Once the blaze is over, the forest – or in this case, the microbiome – has to rebuild from scratch.

“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,” said study co-author Eugene B. Chang.

“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.”

This prompted the team to investigate what happens when both the Western diet and antibiotics team up against the gut.

The experiment started with mice eating either a Western-style diet (WD) or standard mouse chow (RC), the latter being high in plant fibers and low in fat. Both groups were then given antibiotics. Some mice continued on their initial diets, while others switched to the opposite.

The limits of microbial transplants

To speed up microbial recovery, researchers introduced a fecal microbial transplant (FMT). This method is designed to help restore microbial balance by transferring healthy microbes from one animal to another. However, the results were stark.

Only mice fed the RC diet – before or after antibiotics – were able to regain a healthy, balanced gut microbiome. The mice that stuck with or switched to the Western-style diet couldn’t recover. The Western diet seemed to block the microbial transplant from taking hold.

“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 explained. “If the mice are on the wrong diet, the microbes don’t stick, the community doesn’t diversify, and it doesn’t recover.”

Even with the transplant, the Western diet didn’t offer the nutrients needed to support a robust microbial community. These mice also remained highly vulnerable to Salmonella infections.

Preparing your gut for recovery

What’s clear is that food matters – a lot. A diet high in plant-based fiber not only promotes general well-being but may also protect people undergoing harsh treatments like chemotherapy or organ transplants, which often require potent antibiotics and immune-suppressing drugs.

“Maybe we can use diet to rebuild the commensal microbes that have been suppressed under these therapies,” Chang said. “We can restore the healthy microbiome much quicker and prevent the emergence of more multidrug-resistant organisms.”

This isn’t about overhauling your entire lifestyle overnight. The researchers acknowledged that asking everyone to become vegan is neither practical nor necessary. But adding more fruits, vegetables, and whole grains to your meals – especially before surgery or antibiotic treatments – could prepare your gut for a faster, stronger recovery.

Chang is even exploring supplement options that could support gut health without requiring major dietary shifts.

“I’ve become a believer that food can be medicinal,” he 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 key lesson on gut recovery

The message is simple but powerful: what you eat lays the foundation for how your body heals.

When your gut is knocked down – whether by antibiotics, illness, or stress – the right foods can help it get back on its feet. Think of it like this: fruits, vegetables, and whole grains don’t just fill you up – they build you up.

And next time someone reminds you to eat your greens, they just might be saving your gut.

The full study was published in the journal Nature.

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