4 Gut Problems That Trigger Inflammation (Even If You Eat Healthy)

Functional Medicine Practitioner By William Cole, D.C., IFMCP
Functional Medicine Practitioner
Dr. Will Cole, D.C., IFMCP, is a leading functional medicine expert who specializes in clinically investigating underlying factors of chronic disease and customizing a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. Cole is also the bestselling author of Ketotarian and The Inflammation Spectrum.
4 Gut Problems That Trigger Inflammation (Even If You Eat Healthy)

Photo by Stocksy

Ditching processed junk for real, whole foods can do amazing things for our health. I've seen countless cases of lives being improved by the power of food medicine.

But what happens when, after adopting a clean, plant-based lifestyle, you hit a plateau? What happens when your symptoms flare up when you start eating better? I have seen many patients who eat very clean but still have health issues.

There are many possible reasons why eating healthy alone is not enough. But one of the most common underlying issues I often see is found in the microbiome.

Your microbiome is the trillions of bacteria and yeast that live in your gut and on your skin. The microbiome is home to around 80 percent of your immune system and 95 percent of your "happy" neurotransmitter serotonin. Often called your "second brain," it helps control your mood, weight, hormones, and even your genetic expression.

Thousands of years ago, Hippocrates, the father of medicine said, "All disease begins in the gut." Now, science is catching up with antiquity. Because your gut is foundational to almost every other system of your body, if you have a chronic or autoimmune condition, chances are it has at least a microbiome component to it — even if you aren't experiencing digestion symptoms.

If you're eating clean but are still experiencing health issues, there are four underlying gut problems to look for:

1. Leaky gut syndrome

When your intestinal lining is damaged, undigested food particles and bacterial endotoxins called lipopolysaccharides (LPS) can pass through the gut lining, leading to systemic inflammation throughout your body.

In functional medicine, leaky gut syndrome is seen as an almost precondition for autoimmune diseases and many other health problems.

What to do: Eating a clean diet takes out most of the immunoreactive and inflammatory foods like gluten, sugar, and bad fats, which is a great start. There is a chance, though, that years of eating poorly in the past, medications, or just living in a modern toxic world could have caused chronic food intolerances.

When the gut is chronically damaged and an inflammatory-immune response has been triggered, your immune system can react to the healthiest of foods. I have seen bone broth, kale, and just about every other nutrient-dense food be a source of inflammation in some people.

In addition to getting functional medicine labs, an elimination diet is the first step to uncovering food intolerances and healing your gut.

Article continues below

2. Bacterial imbalances

The delicate balance of your gut garden is essential for health. Conditions like small intestinal bacterial overgrowth (SIBO) and other bacterial dysbioses are linked to numerous health problems.

Anxiety and depression have been linked to lower levels of Lactobacillus helveticus and Bifidobacterium longum, and weight gain was linked to higher amounts of Firmicutes.

When someone with dysbiosis or SIBO starts to eat healthier and increases their vegetable intake, it can cause more gut problems, like constipation and bloating. But it is the underlying microbiome issue, not the vegetables, that is the root problem.

What to do: In addition to getting labs done to assess your microbiome levels, you should also consider a FODMAP intolerance. Foods like onions and garlic are just two of the healthy foods that will flare up digestive problems and inflammation in someone with FODMAP intolerance.

Natural antibiotics such as oregano oil, garlic, and uva ursi are some tools I use to help address bacterial overgrowths.

Probiotic combinations of Bifidobacteria, Enterococcus and Lactobacillus have also been shown to have a positive effect on SIBO.

3. Histamine intolerance

One specific intolerance that I often find in people with leaky gut syndrome and bacterial overgrowths is histamine intolerance.

Histamine intolerance occurs when there is a dysfunction or deficiency of the enzymes that break histamines — chemicals produced during an allergic reaction — down. Without the enzymes to effectively get rid of excess histamine, the overflow can cause a lot of problems. There are also foods that naturally contain histamine, or trigger the release of histamine in the body.

What to do: Histamine intolerance can easily be found in people who eat healthfully, because many whole foods are high in histamine.

Fermented foods (kefir, kimchee, sauerkraut, and yogurt, for example), bone broth, and legumes (like chickpeas, beans, soybeans, peanuts) are all foods that are higher in histamine and can trigger inflammation for people with histamine intolerance.

Even with healthy foods, what works for one person may not be right for you.

Article continues below

4. Yeast overgrowth

We all have some yeast in our gut microbiome, but overgrowths of yeast such as Candida albicans can cause chronic low-grade inflammation and immune stress. People with an already weakened immune system or autoimmune problem can find a candida overgrowth to be a trigger for more health problems.

What to do: Fermented foods are generally good for us, but they don't work for everyone. If you have candida or another yeast overgrowth, foods like sauerkraut and kimchee can feed the yeast. Certain probiotic supplements that contain prebiotics can also feed overgrowths.

I generally suggest waiting until after the die-off phase of candida removal before adding these foods back in. This can take anywhere from weeks to months, depending on the severity of the case. For a full list of my tips to fight off candida overgrowth, read my article.

What now? How to achieve optimal gut health:

Do you remember when you started living a healthy lifestyle and it was a little overwhelming? Dealing with microbiome issues might cause the same feelings of "Where do I even start?"

If you feel like you may have one of these gut problems, here are three simple action steps to point you in the direction of health:

Article continues below

Step 1: Consider functional medicine labs.

The first step to the functional medicine approach is finding out the root dysfunctions that give rise to chronic and autoimmune health problems.

Blood and stool labs can give you a detailed look at your microbiome, the levels of your specific bacteria and yeast, rule out leaky gut syndrome, give insight to food intolerances, and measure your autoimmune reactivity.

Step 2. Look at stress levels.

Even if you're eating clean, being chronically stressed can sabotage your body's ability to heal. Chronic stress has been shown to suppress the immune system, decrease blood and oxygen flow to the intestines, and increase gut lining permeability.

Finding ways to regularly de-stress like mindfulness meditation, tai chi, yoga, or just spending time in nature can be a piece to your healing puzzle.

Article continues below

Step 3. Consider personalized functional medicine.

We are all different, and there is no "one size fits all" to regaining your health. If you've cleaned up your diet but still have health problems, I recommend working with a qualified functional medicine practitioner.

Keep in mind that we are all on health journeys. We are all learning what works for our body and what doesn't. Give this journey, and yourself, grace and patience.

William Cole, D.C., IFMCP
William Cole, D.C., IFMCP
Will Cole, D.C., IFMCP, is a leading functional-medicine expert and a Doctor of Chiropractic. He...
Read More
More from the author:
Uncover Hidden Food Intolerances That Wreak Havoc On Your Gut
Check out The Elimination Diet
Regain your energy, vitality and health by tapping into the power of the Elimination Diet with this practical and effective nutrition course.
View the class
William Cole, D.C., IFMCP
William Cole, D.C., IFMCP
Will Cole, D.C., IFMCP, is a leading functional-medicine expert and a...
Read More

More On This Topic

Functional Nutrition Coaching

Functional Nutrition Coaching

Popular Stories

Latest Articles

Latest Articles

Sites We Love

Your article and new folder have been saved!