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Microbiome Health Depends on Your Diet. The Truth to “You Are What You Eat.”

Posted in Our Blog on June 26, 2026

Your microbiome health is quite dependent on your diet. While it might seem like an obvious cause and effect, there are very specific reasons why.

If you eat junk, your body must use that junk to survive. It has a harder time doing it. Likewise, your microbiome has less healthy options to work with. Everything suffers.

If you eat healthy. Fresh fruits and vegetables. Lean meats. Drink plenty of water. Your body tends to be healthier. Your microbiome has all it needs to thrive and protect you from illness, maintain digestion, and improve overall health.

There is truth, after all, to the old adage, “You are what you eat.”

A recent study observed the impact of a modern “Western-style diet” verses a more “Mediterranean diet” on the health of the gut microbiome in mice following recovery from antibiotic treatment.

The outcome was about what you would expect. Further driving the point home, “you are what you eat.”

How Antibiotics Impact Microbiome Health

Antibiotics don’t necessarily target just the pathogenic bacteria. Unfortunately, these medications often work on an entire class of bacteria. Even whole communities of bacteria.

That doesn’t sound like a bad thing, right?

It isn’t.

Not all bacteria are bad. In fact, many are necessary in our natural digestion, are important parts of our immune system, and many serve other microscopic roles.

Senior author Eugene B. Chang, MD likened antibiotics to a forest fire. With our microbiome being the forest. An apt analogy.

“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.”

If the necessary nutrients are not available to the beneficial microbes, those who are not-so-beneficial (or even harmful) can take monopoly on the available resources.

The result?

An imbalance of beneficial microbes. You are more likely to get sick, more likely to have poor digestion, more likely to become nutrient deficient, more likely to experience gas or stomach pain. Microbiome health is important, and it requires balance.

Chang says that the typical Western diet is detrimental to this recovery.

“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.”

So, what exactly is a Western diet?

What is a Western Diet?

The commonly agreed upon term “Western diet” is a diet typically high in red meat, high-fat foods, and refined sugars.

It is loaded with saturated fats, added sugars, and empty calories. Things like processed foods, snacks, and soft drinks. Few fruits and vegetables.

This type of diet is low in fiber, vitamins, and minerals. Nutrients are more likely to be “acellular,” meaning not from cells. Added nutrients, as opposed to those found in food, are harder to digest. Making them more difficult to be used by the body.

People primarily consuming a Western diet have a higher risk of:

  • Metabolic disorders
  • Obesity
  • Diabetes
  • Cardiovascular diseases
  • Depression
  • Anxiety
  • Chronic stress
  • HPA dysregulation
  • Inflammatory bowel disease
  • Cognitive problems (impacting memory, dicision-making, and other important processes)
  • Eating addictive-like behaviors (bingeing fat and sugar)

This study compared the microbiome of mice fed both this Western diet and one closely resembling a Mediterranean diet. Which, presumably, is more beneficial to fostering good microbiome health.

So, what is a Mediterranean diet then?

What is a Mediterranean Diet?

A Mediterranean diet has a greater emphasis on plant-based foods. Things like whole grains, nuts, and legumes. Fruits and vegetables. Foods that are minimally processed, locally grown (if possible).

Meat proteins often come as fish and poultry. However, consumption is low to moderate, with these offerings consumed only a few times a week.

Cheese and yogurt are big in the Mediterranean diet, with olive oil as the principal source of fat.

Instead of causing many of the above issues found in those consuming a Western diet, the Mediterranean diet has shown to reduce those risks.

Those consuming a Mediterranean did have reduced risk of heart disease, metabolic syndrome, diabetes, depression, certain cancers, and decrease risk of frailty in older adults.

How Did Diet Impact Microbiome Health?

This study analyzed the microbes found in the digestive system of mice both before and after given antibiotic treatment. Some mice were fed a Western diet, while others were fed regular mouse chow (closely matched to Mediterranean diet). Some were given a fecal microbial transplant (FMT), which essentially is a direct dose of beneficial bacteria.

How did they perform?

According to the paper, mice consuming the Mediterranean style diet before or after antibiotics were able to recover a healthy microbiome equilibrium. Researchers assess that this diet promotes formation of metabolites from food that the healthy microbes can use to build a healthy ecosystem.

Those on the Western diet did not perform as well. Even after given a FMT to help restore microbiome health, it didn’t take.

“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.”

A Great Time to Look at Our Own Diets for Microbiome Health

Does your diet more closely resemble a Western diet? Or a Mediterranean one? We all know fruits and vegetables are healthy. We all know processed foods are generally not. The Western diet is certainly more convenient and often more accessible. But the Mediterranean diet can be packed full of flavor too.

It is a great time to take a closer look at the things we eat. Are they good for us? Are they good for our microbiome? Will we feel better after eating it?

Stay in Touch with Make Food Safe!

If you’d like to know more about food safety topics in the news, like “Microbiome Health Depends on Your Diet. The Truth to “You Are What You Eat.”,” check out the Make Food Safe Blog. We regularly update trending topics, foodborne infections in the news, recalls, and more! Stay tuned for quality information to help keep your family safe, while The Lange Law Firm, PLLC strives to Make Food Safe!

By: Heather Van Tassell (contributing writer, non-lawyer)