The Connection Between Autoimmune Disease and Gut Bacteria

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Autoimmune diseases, like most chronic diseases, are on the rise. It’s now estimated that 50 million Americans suffer from an autoimmune disease, which roughly breaks down to 20% of the population.

But Americans are not the only ones suffering. We’re actually witnessing an increase in autoimmune disease all across the globe particularly over the last 10 years in developed countries. So, what’s happening here? 

There are many possible causes for the development of an autoimmune disease. In this article, I’m going to discuss how a poor diet coupled with chronic stress and increased environmental toxicity can lead to increased intestinal permeability or leaky gut. Leaky gut then leads to immune dysfunction, which sets the stage for an autoimmune disease to develop and progress.

Immunity 101

When the body is healthy, the immune system does an excellent job protecting the body from invaders. It produces antibodies against viruses, bacteria, parasites, and other pathogens, and these antibodies help keep infections under control. An autoimmune disease develops when the immune system mistakenly produces autoantibodies (immune cells) directed against human cells, tissues, or organs. 

These autoantibodies and other aberrant immune cells begin to attack, depending on the particular type of autoimmune disease, certain parts of the body. In a general sense, autoimmunity can result in damage to the following:

  • Skin
  • Brain
  • Joints
  • Muscles
  • Intestines
  • Nerves
  • Other tissues and organs

It has now been established that there are over 80 classified autoimmune diseases, some being rarer than others. Below are examples of common autoimmune diseases that I regularly see in practice:

  • Hashimoto’s thyroiditis
  • Rheumatoid arthritis
  • Scleroderma
  • Diabetes, type I
  • Multiple sclerosis
  • Celiac disease
  • Crohn’s disease
  • Ulcerative colitis
  • Lupus
  • Eosinophilic esophagitis
  • Grave’s disease
  • Lichen sclerosis
  • Psoriasis

How Do I Know if I Have an Autoimmune Disease?

If you are developing strange and unexplained symptoms that are progressing in severity and frequency or tend to wax and wane with no identifiable cause or pattern, then you may want to see your doctor for further workup. Also, if your doctor reports that your symptoms are “atypical,” then consider autoimmune disease as an underlying etiology. 

Signs and symptoms can vary tremendously, again, depending on the type of autoimmune disease, but below are some of the more common signs and symptoms that may present:

  • Joint swelling and pain
  • Muscle pain
  • Skin rashes
  • Fatigue
  • Cognitive dysfunction or trouble concentrating
  • Hair loss
  • Numbness or tingling in hands/feet
  • Digestive issues
  • Swollen glands
  • Low-grade fever

There are many lab tests that will help to identify an underlying autoimmune condition. Antinuclear antibody (ANA) is a common screening antibody for autoimmune diseases like lupus or scleroderma. 

If you are complaining of joint pain your doctor may run rheumatoid factor (RF), cyclic citrullinated peptide (CCP), and a host of inflammatory markers like erythrocyte sedimentation rate (ESR) or C-reactive protein (CRP).  These markers would help rule out an autoimmune condition like rheumatoid arthritis. 

If you’re experiencing thyroid symptoms and your thyroid markers like TSH are all over the place, your doctor may run anti-tissue transglutaminase (TTG) and antithyroglobulin (TG) autoantibodies, which would investigate whether you have Hashimoto’s thyroiditis: an autoimmune condition affecting the thyroid gland.   

As you can imagine, diagnosing an autoimmune condition can be tricky and is not always black or white. There can often be lots of crossover with other conditions, and other autoimmune conditions for that matter.    

The good news is if you develop an autoimmune disease, it is possible to reverse the development and progression depending on many factors. The truth is I’ve seen many cases of autoimmunity resolve with proper dietary and lifestyle changes with targeted nutritional and herbal medicine support.

How Leaky Gut Can Lead to Autoimmunity

I’ve written a lot about leaky gut and how this condition can cause not only symptoms within the GI tract but also systemic symptoms as well. Think of leaky gut as a major player in the development of autoimmune disease. 

Normally cells lining the intestines are tightly joined together like solders standing arm to arm. These tightly joined cells form a thin barrier that keeps unwanted substances within the GI tract. 

With chronic stress, poor dietary habits like sugar and processed food consumption, and exposure to environmental toxins like glyphosate, the tightly joined wall of cells break apart and foreign substances like bacterium, breakdown products of foods, and toxins can now freely enter the surrounding tissue and bloodstream. 

As these substances enter the surrounding tissue and bloodstream, the immune system is activated and it begins to produce immune cells including antibodies against these foreign invaders (antigens). Sometimes, the immune system gets confused and begins to attack human tissue instead of the antigen. They call this phenomenon molecular mimicry, which is when a foreign antigen shares similar structural similarities to self-antigens.  

The resulting effect is immune system over-activation against self-antigens or human tissue, and inflammation ensues. Immune complexes can form and deposit anywhere in the body, like in the joints for example, causing a lot of pain (think rheumatoid arthritis). Or, in a condition like Hashimoto’s thyroiditis, the body’s immune system can accidentally attack the thyroid gland instead of going after the gluten protein.

Unless the leaky gut is repaired, this vicious cycle of immune activation and dysfunction will prevail and symptoms of autoimmune disease will continue.

The Way I Approach Autoimmune Disease: Heal the Gut

With any case of autoimmune disease, I work on healing the gut and also address the underlying immune system dysfunction. It can take 6 months or longer to see big changes, but often symptoms improve within a couple of weeks. This symptom improvement is what drives people to stay the diet and continue to heal their gut and immune system. 

Diet changes will certainly be the largest hurdle for you, but don’t fret as I’m asking you to do this diet for only one month and then see how your body feels. Some of the foods below will, of course, be able to be included back into your diet, but it’s VERY important to stay completely away from them. Make sure you especially refrain from eating the gluten-containing grains as even a small amount of gluten can damage your intestinal wall preventing you from healing leaky gut. 


Here are some major dietary changes (for one month or longer) that I recommend for those suffering with an autoimmune disease.

You want to eliminate:

  • Grains, including gluten-free grains
  • Legumes (lentils, beans, etc.)
  • Dairy products
  • Nightshade vegetables (potatoes, peppers, tomatoes, eggplant)
  • Sugar-containing foods (fruit is OKAY, as are very small amounts of honey or maple syrup)
  • Eggs
  • Alcohol and caffeine

Now before you run for the hills, let me explain a couple of things: This massive diet overall (i.e. elimination diet) is designed to remove all the major food allergens/intolerances so that your immune system has a chance to reset and calm down. Leaky gut will also be improved. After a couple of weeks on this diet, you will likely see some of the autoimmune symptoms reduce in severity and frequency. As time goes on, more and more may completely resolve. 

You’re probably asking yourself “well what CAN I eat?” Basically, lots and lots of vegetables:

  • Vegetables (except nightshades)
  • Fruits
  • Nuts/seeds (in moderation, and soaked is best)
  • High-quality meats and fish
  • Healthy fats


It’s also very important to tame the stress in your life.  An acute stressor will do no harm to your digestive tract, but chronic long-term stress can weaken the intestinal barrier leading to leaky gut and immune dysfunction.  You may want to engage in some or all of the following mind/body medicine practices to calm down the stress response:

  • Meditation
  • Slow rhythmic belly breathing
  • Yoga
  • Walks in nature
  • Massage/acupuncture/body work


There are many environmental toxins like heavy metals, molds/mycotoxins, and industrial and/or agricultural chemicals that can trigger autoimmunity.  It is important to avoid these and other toxins as much as possible. For example, glyphosate, a ubiquitous herbicide-like compound found in many foods, can trigger zonulin release in the intestine, which can predispose you to leaky gut. It’s recommended to eat as much organic food as possible (which typically registers lower for glyphosate counts), and stay away from GMO foods. 

The bottom line is treating a leaky gut can lead to a drastic improvement in autoimmune symptoms. In medicine, I am always amazed at how powerful a clean diet can transform someone from sickness into health. Although a radical change in diet can be challenging, it is the most supportive therapy I’ve found for treating autoimmune disease.


Dr. Drew Sinatra

Meet Dr. Drew Sinatra

Dr. Drew Sinatra is a board-certified naturopathic doctor and self-described “health detective” with a passion for promoting natural healing, wellness, and improving quality of life by addressing the root cause of illness in patients of all ages. His vibrant practice focuses on treating the whole person (mind, body, and spirit) and finding missed connections between symptoms and health issues that are often overlooked by conventional medicine.

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