August 14, 2023

The Gut-Immune Connection: 8 Ways to Strengthen Your Gut Microbiome

photo of Tom Gerencer

Written By

Tom Gerencer

photo of Mary Stratos, PA-C, IFMCP

Medically Reviewed By

Mary Stratos, PA-C, IFMCP

Lifeforce Physician Assistant

The Gut-Immune Connection: 8 Ways to Strengthen Your Gut Microbiome

When we were young, many of us ate whatever we liked without thinking twice. But as we enter our 30s and beyond, the check-engine light comes on. And there’s no sugar-coating it: Today, we're learning that many chronic diseases are driven by low-grade systemic inflammation, and that it might be tied directly to our gut.

To explore this new field of science — and what it means for our health — Lifeforce spoke with Emeran Mayer, MD, Executive Director of the UCLA Center for Neurobiology of Stress, and bestselling author of The Mind-Gut Connection: How the Hidden Conversation Within Our Bodies Impacts Our Mood, Our Choices, and Our Overall Health and The Gut-Immune Connection, How Understanding the Connection Between Food and Immunity Can Help Us Regain Our Health

Keep reading to learn more about how our food choices impact our gut microbiome, and how we can use this new knowledge to gut-check our health. 

You Ache What You Eat

The standard American diet — ultra-processed, high in sugar, and low in fiber — appears to play a major role in changing the composition of the microbial ecosystems in our gut.

“Our diet has changed dramatically in the last 75 years,” says Dr. Mayer. “Our microbes have adapted, but our own genes can’t adapt that fast. So, our immune cells in the gut look at the new microbes and say, ‘something is wrong.’ The altered microbiome also changes the integrity of the intestinal barrier between the microbes and the gut-based immune system. As a consequence, the immune cells are ringing the alarm bells, triggering an immune response. That’s why we have this chronic engagement of low-grade inflammatory responses.”

“Normally,” says Dr. Mayer, “our gut microbes are separated from our immune system by a layer of mucus and a layer of tightly linked cells. But we now believe our modern diet and chronic stress can compromise that barrier.” When that happens, our gut microbes can come into contact with sensors on certain immune cells that “extend their tentacles” into the mucus layer. “This triggers a reaction by the gut-based immune cells right on the other side of the barrier, which can lead to further increases in permeability, allowing entire microbial cells to pass into the gut-associated immune system. The resulting release of immune mediators can make the gut lining even more permeable, and can spread low-grade inflammation throughout the body.”

Emeran Mayer Books | LifeforcePoor Gut Health Drives Inflammation and Disease

The chronic immune system activation that the modern lifestyle encourages may show up as a laundry list of inflammation-based diseases, including:

  • Eczema

  • Mood changes

  • Allergies

  • Alzheimer's disease

  • Chronic heart disease

  • Liver disease

  • Colon cancer

  • Parkinson's disease

“I think that to a certain degree,” says Dr. Mayer, “the risk for many of these diseases in genetically vulnerable individuals is increased by the mismatch that has developed between the gut microbiota and the immune system.”

Gut Microbiome | LifeforceYour Health Starts at Childbirth

Research has shown that C-section babies don't get the same dose of vaginal and fecal microbes as babies born by vaginal delivery. 

“While that difference eventually self-corrects, that initial year plays a big role in programming the immune system,” says Dr. Mayer. “For instance, there's a higher rate of asthma, autoimmune disorders, and obesity in children born by C-section. What is emerging as a very attractive hypothesis is that alterations in the brain happen early, while the fetus is still in the womb and is exposed to molecules coming from the mother's microbiome.” 

So, if the mother consumes the standard American diet and has low-grade inflammation, these inflammatory molecules may get through the placenta and compromise the brain development of the fetus. That can set us on the path to inflammation-based diseases from day one.

purple cabbage gut health | LifeforceWays to Strengthen Your Gut Microbiome

While that may all sound bleak, it also shines a ray of hope on our future health. By choosing fewer processed foods and a wide variety of vegetables and fruits, we can help support a healthier microbiome. That said, not all healthy changes are as intuitive — like getting more high-quality social interaction or regularly consuming a diet rich in naturally fermented foods..

1. Avoid Ultra-Processed Foods

“We know vegetarians generally live longer and have fewer chronic health problems,” says Dr. Mayer. “So you could say that animal products are the main culprit. But then you can look at countries like Argentina or Brazil where these health problems aren’t as prevalent, even though the people there consume very large amounts of red meat.”

Dr. Mayer speculates that this difference has to do with how the cows are raised in those countries, (free roaming, grass fed), and how their meat is processed.

“I personally believe that the ultra-processing in the U.S. is a big component of our chronic health epidemic, even among foods we think are healthy, such as organic granola bars or other so-called natural packaged foods,” notes Dr. Mayer. 

2. Choose More Prebiotic Foods

The more fiber in your diet, the more food your gut microbiota have to thrive on. Prebiotics are the different types of fiber and other food ingredients that feed your microbes. So, instead of choosing processed foods (that generally have reduced prebiotic content) eat foods like:

  • Oats

  • Fruits

  • Vegetables

  • Rice

  • Beans

  • Seeds

  • Nuts

Eating vegetables raw at times may help diversify your gut microbiota. In fact, some foods (like plain raw cabbage) contain natural probiotics that are killed by cooking them. While these organisms are present in only small amounts, there’s some speculation that they may help repopulate your gut with a wider range of species types.

3. Eat a Wider Variety

“It's not rocket science,” says Dr. Mayer. “You don’t have to eat an exclusively plant-based diet, but eat a largely plant-based diet, with a wide variety of different fruits and vegetables.”

Dr. Mayer recommends eating 15 different vegetables or fruits each week to maximize the prebiotic effects of your diet.

“Each of these foods has different fiber molecules in them, requiring different specialist microbes to break them down. So you force your microbial ecosystem, you could say, to ‘hire’ more specialists to do the job, basically increasing your gut microbe diversity, and supporting optimal health.”

fermented foods for gut health | Lifeforce4. Eat More Fermented Foods

Fermented foods have been a way of life for millennia. Then in the 1950s, refrigeration erased these health boosters from the menu.

“Probiotic supplements have received a lot of attention in the media and in social media,” says Dr. Mayer. “And though evidence from controlled, high-quality studies is missing, they’re thought to be beneficial. However, recent research shows a significant health benefit and inflammation-fighting benefit from eating a variety of fermented foods.”

“But if you think about it, people started to ferment foods as a way to preserve them, thousands of years ago. And every time something has been around for thousands of years, there's been enough time for our genes to adapt to it.”

In Dr. Mayer’s view, our bodies have evolved to eat fermented foods, and suddenly taking them away may negatively affect our health.

See 9 more ways to boost your longevity in our article 10 Longevity Hacks to Live Longer and Stronger.

5. Eat More Organic Foods

You probably know organic foods are “good for you,” but knowing the reason might make it easier for you to make important healthy choices.

Certain pesticides like Glyphosate can kill off important organisms in your microbiome, like Lactobacillus, Butyricoccus, and Ruminococcaceae. This can in turn reduce the key compounds (metabolites) that our microbiomes produce.

For example, Ruminococcaceae generates metabolites that are important for liver health, brain health, and energy production, while Butyricicoccus helps stave off inflammatory bowel disease. Lactobacillus, meanwhile, has been shown to help prevent cancer and regulate immunity

So, choosing organic foods isn’t just a good idea that may help you many years from now. If you want to optimize your energy and health today, selecting more expensive organic options can be as vital as taking the right supplements — maybe even more so.

At the very least, choose organic versions of the “dirty dozen” — foods with the highest pesticide content:

  1. Strawberries

  2. Spinach

  3. Kale, collard greens, mustard greens

  4. Peaches

  5. Pears

  6. Nectarines

  7. Apples

  8. Grapes

  9. Bell & hot peppers

  10. Cherries

  11. Blueberries

  12. Green beans

6. Eat Less Meat

The amount of meat you eat may also play a major role in your health.

“The quantity of meat consumption has definitely increased,” says Dr. Mayer. “People couldn't afford to eat as much meat 50 years ago. But today it's cheaper to have dinner with your kids in a McDonald's, with everyone eating a hamburger, than to take the time to prepare a healthy meal.”

While Dr. Mayer doesn’t advocate vegetarianism, his many decades of research have led him to believe that minimizing meat consumption may help promote a healthy gut microbe ecosystem.

7. Manage Your Stress

Surprisingly, diet isn’t the only driver of a healthy gut. According to Dr. Mayer, severe or chronic stress can thin the mucus layer in your stomach and intestines, causing inappropriate immune activation. This can in turn affect our stress levels in a downward spiral.

“Stress levels have been shown to change our gut’s immune system, epithelial barrier, and microbial composition,” Dr. Mayer says. “The ultimate outcome is increased gut permeability and low-grade inflammation, and a compromise of the gut microbial ecosystem diversity and richness. But that in turn can alter the brain and lead to depression-like behavior.”

Managing your stress through quiet time, meditation, exercise, and mindfulness practice aren’t just good for your emotions. They can also give you a healthier gut and less inflammation, which may keep you safer from disease, says Dr. Mayer.

8. Get More Social Interaction

Believe it or not, social interaction may impact the helpful creatures living in your gut.

“Over and over again,” says Dr. Mayer, “the authors of studies about the Mediterranean diet have emphasized the importance of close social interactions in their study outcomes. In Italy, Spain, and other Mediterranean countries, every evening people sit outside and eat together and enjoy each others’ company.”

This is another healthy practice that has been falling apart in the U.S. “If you have to commute to work for an hour and a half, you don't have time to have breakfast with your family. And then when you come home, you're certainly not in a position to socialize with friends each day.”

In fact, the U.S. Surgeon General has recently announced an epidemic of loneliness and social isolation.

Making time for meals with family and friends may not be just a fun idea. It may ultimately help decide how long you live — and the quality of your health along the way. In fact, “blue zone” communities, where people live longer, healthier lives, prioritize time with loved ones. Read more in our article: 9 Healthy Habits from Blue Zones to Live Better, Longer.

To learn more, listen to Dr. Mayer’s podcast The Mind Gut Conversation here, or sign up for his weekly newsletter here. You can also follow him on Instagram at @emeranmayer, order his bestselling books The Mind Gut Connection and The Gut-Immune Connection, or preorder his upcoming recipe book Interconnected Plates, available at

This article was medically reviewed by:
Mary Stratos, PA-C, Institute for Functional Medicine Certified Practitioner

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