gut diversity | Integrative functional medicine blog

Autoimmunity and leaky gut




Autoimmunity, a disorder in which the immune system attacks and destroys body tissue, is one of the most prevalent diseases today, affecting predominantly women. In fact, about 75% of all autoimmune disease occur in women.

Traditionally, autoimmune disease was thought to be primarily a genetic disease, but research increasingly shows that while genetics play a role, intestinal permeability, or leaky gut, is also an important factor. This means your diet can determine whether you develop autoimmunity.

A great saying in the the “functional medicine” world is
“genetics load the gun, environment pulls the trigger.”


Examples of common autoimmune diseases include:

  • Type 1 diabetes
  • Celiac disease
  • Multiple sclerosis
  • Crohn’s disease
  • Hashimoto’s hypothyroidism
  • Psoriasis
  • Rheumatoid arthritis
  • Vitiligo

Leaky gut triggers autoimmunity

Leaky gut is a condition in which the lining of the intestines become damaged and overly porous, allowing bacteria, yeast, undigested foods, and other pathogens into the bloodstream where they trigger inflammation and an over reaction of the immune system.

Leaky gut keeps the immune system in a hyper zealous state. This eventually makes the immune system more likely to start attacking the body tissue it was designed to protect, causing an
autoimmune condition. Think of it kind of like the incredible hulk. Once he turns into that raging green beast he is not selective in who and/or what he destroys. He will attack pretty much whatever is in the way.


People can develop leaky gut for a variety of reasons, but the most common is linked to inflammatory foods in the diet. These can include too much sugar, processed foods, junk foods, and fast foods. Also, many people have undiagnosed food sensitivities, such as to gluten, dairy, egg, or other foods. These can damage the gut lining if you have an inflammatory reaction to them.


Gluten, in particular, is notorious for its ability to cause leaky gut and trigger autoimmunity. In people who have a gluten intolerance, gluten triggers inflammation in the gut and elsewhere in the body every time they eat it. In gluten sensitive individuals, gluten also acts on messenger compounds in the intestinal wall to make it more permeable. This allows more inflammatory factors into the bloodstream, including more gluten, in a self-perpetuating vicious cycle.

There are even test we can do to test if you have leaky gut.



For some people, simply going gluten-free can repair a leaky gut and dampen autoimmunity.


Other causes of leaky gut that trigger autoimmunity
Knowing why you have leaky gut is an important strategy in not only in repairing it, but also in dampening autoimmunity. Below are some known causes of leaky gut that can, in turn, trigger autoimmunity:

  • Gluten sensitivity
  • Inflammatory foods (sugars, junk foods, fast foods, etc.)
  • Alcohol
  • Medications (corticosteroids, antibiotics, antacids, some arthritis medications)
  • Infections (poor gut bacteria balance, H. pylori, small intestinal bacterial overgrowth, yeast, parasites, and viruses)
  • Chronic stress
  • Hormone imbalances
  • Processed foods, artificial food additives, thickening gums
  • Environmental toxins
  • Vitamin D deficiency
  • Autoimmunity (although leaky gut triggers autoimmunity, autoimmunity can also cause leaky gut, especially if the immune attack is against tissues of the gut)

If you have an autoimmune disease, you have leaky gut. If you have leaky gut, you have or will get an autoimmune disease. It’s just a matter of time.

I’m Dr. Craig Mortensen
Be healthy, be happy!

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Spore probiotics for your gut microbiome




As we continue to learn how important healthy gut bacteria is for the brain and immune system, interest in cultivating a rich and diverse “gut microbiome” grows.

One important tool in this quest are
spore-based probiotic supplements. “Spore” is derived from the word “seed,” and spore-based probiotics are a hardy delivery system that germinate in the small intestine and help you colonize your gut with more healthy bacteria.


Modern humans face many challenges to developing and maintaining healthy gut bacteria. In fact, studies of primitive people who live much like our hunter gatherer ancestors did show their guts have about 50 percent more diversity in gut bacteria than the average American. Its not just how much good bacteria you have, it’s how many different types.

Researchers are finding this lack of microbiome diversity plays a role in many chronic health and brain disorders, including depression and autoimmunity.

This is often one of the reasons I recommend periodically switching probiotic brands and strains. Diversity.


Low-fiber, junk food diets, antibiotic overuse, chlorinated water, heavy environmental toxin and pollution loads, chronic stress, alcohol, and various medications all play a role in reducing the diversity and amount of beneficial gut bacteria.

As a result, opportunistic and infectious “bad” gut bacteria are able to more easily conquer the gut. This weakens the gut lining, increases inflammation, and promotes brain and mood disorders.


There are many ways we can build a healthy and diverse population of gut bacteria. The most important is to eat a whole foods diet that is predominantly vegetables and fruits.
It’s important to vary the kind of produce you eat regularly. It’s also helpful to include cultured and fermented foods and take probiotics. Also, avoid drugs such as antibiotics, NSAIDs, and heartburn medication as much as possible, which can also contribute to the development of leaky gut, among other things.


Given the challenges the modern gut faces, it’s not a bad idea to make probiotics a part of your routine. This is where
spore-based probiotics come in. What makes spore-based probiotics special?

  • The survive the acidic environment of the stomach on their way to the intestines.
  • They resist breakdown by digestive enzymes.
  • They are heat stable and don’t need to be stored in the refrigerator.
  • Some spores are antibiotic-resistant, which means you can take while taking antibiotics.

Once in the small intestine, spore-based probiotics can germinate,
if you provide the right environment with plenty of plant fiber.


Spore probiotics and healthy gut bacteria in general can help improve your health in several ways. They improve the health and integrity of the lining of the small intestine. This lining contains not only bacteria but also plenty of immune cells to defend the bloodstream from bad bacteria, yeast, toxins, undigested foods, and other pathogens that can trigger inflammation if they make their way through the gut lining into the bloodstream. This is called leaky gut.


For instance, one strain of
spore-based probiotic, bacillus coagulans, has been well studied for its beneficial effect on irritable bowel syndrome (IBS) and Crohn’s disease.

Bacillus coagulans produces lactic acid, which has been shown to help protect the gut and boost immune resistance to viruses. It has also been shown to lower cholesterol and reduce pain and stiffness associated with arthritis.

Ask my office for more information on how to support healthy gut bacteria and help eradicate bad bacteria to improve immune health.

Now go eat something new, go eat some dirt, get exposed to some new healthy bacteria.

I’m Dr. Craig Mortensen
Be healthy, he happy!

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