Gut Health and Autoimmune Disorders |Review


This is a thorough review to know the link between gut health and autoimmune disorders. Do you suffer from rheumatoid arthritis, lupus, type 1 diabetes, multiple sclerosis or any other chronic inflammation or autoimmune and degenerative disorder? Recent studies have shown that the root of the inflammation and autoimmunity might be at the gut. It all starts with the inflammation of the gut that produces an autoimmune response in the body´s own tissues over time.

Is it possible that the root of the problem of autoimmune disorders might start at the gut? Keep reading to know how the lost of gut health is the real problem that has generated chronic inflammation and autoimmunity over time.

Gut Health and Autoimmune Disorders |Review

Gut Health and Autoimmune Disorders

The link between gut inflammation and autoimmune diseasesOrange dots represent the gut bacterium E. Gallinarum in liver tissue.

This image belongs to the research team at Yale University. I give full credit for this image to Yale University research team copyright owner. I leave stated that “no copyright infringement is intended” and I´m using it only for educational purposes.

The link between gut inflammation and autoimmune diseases

There is evidence-based medicine to know that there really is a link between gut inflammation and autoimmune diseases. There is a study (1, 2) published in the journal Science on March 9, 2018, that was made by medical doctors at Yale University. Dr Martin Kriegel, Adjunct Assistant Professor of Immunobiology at Yale School of Medicine and his research team discovered a gut bacterium called Enterococcus gallinarum in liver tissue of humans and mice.

Dr. Kriegel and his Yale research team found that the gut bacterium, E. gallinarum translocated to other organs outside the gut such as the lymph nodes, liver and spleen. It generated auto-antibodies and inflammation, in other words, an autoimmune response. They found the same bacteria in liver cells of patients with autoimmune diseases such as lupus and autoimmune liver disease.

They discovered that giving an antibiotic and a vaccine aimed at E. gallinarum, the autoimmune response was suppressed in mice. This is great news for patients with lupus and other autoimmune diseases if they could suppress their autoimmune disorder just by taking an antibiotic and a vaccine.

Another study showed that a specie of Lactobacillus probiotics given to lupus mice supressed the inflammation. Also, there is another study which showed that giving antibiotics to lupus mice, removed harmful bacteria form gut microbiota and ameliorated the lupus symptoms.

There appears to be a link between gut health and type1 diabetes. There is evidence-based medicine in another study that shows healthy gut microbiota regulates the immune response but, a dysbiosis or alterations in the gut good bacteria can promote autoimmunity. They observed that the presence of a gut bacterium called Bacteroides is protective against Inflammatory Bowel Disease (IBD). They also observed that a protein expressed by the Bacteroides is almost identical to a protein expressed by insullin-producing cells in the pancreas. Therefore, the CD8 lymphocytes could mistakenly attack the pancreatic cells and cause type 1 diabetes.

There is evidence-based medicine that supports the existence of the gut-brain connection. There is another study that shows a link between gut bacteria and Multiple Sclerosis. They found that patients with Multiple Sclerosis had four times more amount of Acinetobacter calcoaceticus and Akkermansia muciniphila. Besides, they had one quarter the amount of Parabacteroides distasonis compared to healthy people. Then, they took their research further and they injected gut bacteria from Multiple Sclerosis patients to mice and they also developed severe brain inflammation.

I´m excited to see what future investigations might bring new improvements for the treatment of patients with lupus, type 1 diabetes and autoimmune diseases.

Gut-Brain Connection. Gut Health and Autoimmune Disorders |Review

Dr. Aristo Vojdani, (PhD, MSc, MT), clinical director of Immunscience Laboratory, is one of the head functional immunologist in the world. He shared with us at the IBS and SIBO Summit the following advice: “when we don´t detect gut disfuntion at an early stage, the end result could be autoimmunity and degenerative disorders like multiple sclerosis and Alzheimer´s Disease.” He explained really well the difference between food allergy and food intolerance in a way that we can better understand this disorders.

Food Allergy vs Food Intolerance

It´s important to differenciate food allergy vs food intolerance or non IgE (Immunoglobulin E) mediated immune reactivity.

Food allergy occurs because people become allergic to any substance, like shrimp or peanuts for instance, they produce high levels of IgE which activates the mast cells to release histamine, leucotrienes and cytokines. It produces a type 1 hypersensitivity so that, can produce a severe reaction such as an anaphilactic shock. Therefore, it is very important to make the allergy tests to identify the substance that causes the allergy.

Food intolerance or IgG food immune reactivity, on the other hand, occurs with another mechanism. The gut flora develops within the first 2 years of life and it changes over time depending on environmental factors. IgA is the first antibody that appears in the immune system of all babies as the first line of defense. Upon antigens (breast milk, bacteria, environmental antigens) the immune system starts its function and the first antibody that appears is IgA. The immune system also has T regular cells, those cells learn to live in harmony with the milk and food and friendly bacteria.

If these cells don´t develop correctly and the gut flora changes over time causing a disbalance in the gut bacteria, this would be detrimental to the gut generating classical allergies or immune reactivity. They induce immune intolerance to the food that is consumed and to the gut bacteria. As a consequence, the food might not be digested properly and there is a release of inflammatory cytokines in the gut, bacteria overgrowth, release of toxins, and now the undigested food and bacteria go through the intestine wall into the blood stream where the antigen presenting cells along with B cells and T cells will induce the generation of antibodies IgA and IgG against food and bacteria.

If this process of food intolerance continues over time, the result will be immune disease in the future such as rheumatoid arthritis, lupus or autoimmune disorders, just to name a few. Some types of food and bacteria can mimic our tissue so, when the immune system attacks the food and bacteria, the same antibodies also attack the own body´s tissue resulting in autoimmunity in the future.

Gut Health and Autoimmune Disorders |Review

Alterations of the gut lining by a gut bacterium, E. gallinarum.

This image belongs Manfredo Vieira et al. and his research team, Science 2018. I give full credit for this image to Manfredo Vieira and his research team copyright owner. I leave stated that “no copyright infringement is intended” and I´m using it only for educational purposes. I found the image at researchfeatures.com.

What are the causes of leaky gut?

When the intestine wall lining is altered by different mechanism, the food and intestine particles, bacteria, virus, parasites can go into the bloodstream generating the production of antibodies against these antigens. The antigens can mimic the body´s own tissue and the antibodies end up mistakenly attacking own tissue that can be maintained over time, in other words, the consequence is an autoimmune response in the future. Leaky gut might be present in different disorders such as:

  • Irritable Bowel Syndrome (IBS)
  • Small Intestine Bacteria Overgrowth (SIBO)
  • Chron´s Disease
  • Ulcerative Colitis
  • Celiac Disease
  • Non Celiac Gluten Sensitivity
  • Non IgE mediated food immune reactivity

Bacteria Bacteroides fragilis, one of the main good bacteria of the gut microbiome in humans.

What triggers the gut inflammation dysbiosis?

The human body, specially the gut, is colonized by many microbes which are called the microbiota. It is necessary that a number of good bacteria microbiota exist in the gut for a healthy life. Sometimes, environmental factors in the presence of genetic factors can alter the microbiota and generate a dysbiosis that can produce chronic inflammation and autoimmunity over time in the future. Some factors that can trigger the gut inflammation dysbiosis are:

  • Undigested food (a bad diet with too much sugar, bad fats and processed foods, junk food, lack of fruits, vegetables and antioxidants in the diet, genetically modified ingredients, gluten and dairy, alcohol)
  • Toxic chemicals in water and evironmental toxins such as pesticides, BPA from plastics, mercury.
  • Oral infections (gingivitis, periodontitis)
  • Gastrointestinal infections (bacteria, virus, fungi such as Candida overgrowth, parasites)
  • Medications alter the good microbiota (antibiotics, NSAIDS, acid-reducing drugs, steroids)
  • Chronic stress (physical or psychological such as depression or anxiety can weaken your immune system over time)
  • Genetics

How can we check for leaky gut?

How can we check for leaky gut?

When you have a healthy gut, the tight junctions at the intestine wall only allow to pass into the bloodstream nutrients needed for a healthy life. However, when the gut is affected by chronic inflammation, those tight junctions become loose, the intestine lining is altered and bigger particles of undigested food, toxins, virus or bacteria in the intestine can pass through to the bloodstream, and that can be measured through different techniques that Dr. Vojdani explained at the IBS and SIBO Summit, such as follows:

  • Intestinal Barrier Dysfunction for Macro-molecules
    • This test measures antibodies against macro-molecules: Lipopolisacharides, ti-junction proteins, food antigens, bacterial toxins, citoskeleton structure of the intestine cell.
    • If the patient is making IgE, IgA, or IgG against any of these macro-molecules, that´s an indication of a leaky gut.
  • Lactulose-Manitol test.
    • The patient is given a mixture of lactulose (double sugar) and a mixture of manitol (single sugar) the manitol will pass through the intestine wall but, if the person has a leaky gut, both lactulose and manitol will pass through.

Gut Health and Autoimmune Disorders |Review

Is leaky gut an autoimmune disease?

80% of your immune system is located in your gut so, there is where chronic inflammation and the immune response starts to take place when the particles from the intestine go through the intestine wall to the bloodstream and start the production of antibodies that in the future might produce an autoimmune disorder in other tissues.

Gut Health and Autoimmune Disorders |Review

Can leaky gut generate autoimmunity over time?

Dr. Aristo Vojdani explained at the IBS and SIBO Summit that, the more we get exposed to environmental factors, the more we will generate antibodies IgA, IgG, IgE against those factors. Dr. Vojdani is the creator of the Elisa test, he says that this test he developed many years ago (1980´s) has many false positives and false negatives for different food antibodies and, all the laboratories keep doing this first Elisa test he created so, he strongly discourages the use of this Elisa IgG test for that purpose.

A few years ago, after 5 years of research, Dr. Vojdani developed an optimized Elisa test at Cyrex Lab and Immunosciences Laboratory which has less false positives and less false negatives. Also, he testes for duplicates and they have to match, otherwise he repeats the test. He added testing for cooked foods as well as raw foods because some people might react to raw food but not to cooked food or otherwise.

Food IgG testing against specific types of food (shrimp, milk, peanuts) will reveal the amount of antibodies against each food. Under normal conditions, there should be small amounts of IgG, IgA and IgE against everything. When the antibodies are too elevated (10 times more) is when the tolerance mechanism has broken down and, if you don´t remove the food from the patient, there is a risk that will develop autoimmunity in the future.

For instance, if a person reacted to milk, will generate antibodies IgG against milk proteins: alpha casein and beta casein. They will cross-react with brain cells glycoproteins. Therefore, if you remove dairy products from the diet of a person who reacted to milk antibodies, you will save that person from suffering autoimmunity and degenerative problems in the future such as multiple sclerosis like syndrome.

Gut Health and Autoimmune Disorders |Review

My final opinion

There is enough evidence-based medicine to know that chronic inflammation starts at the gut and it can generate over time an autoimmune response in other tissues. It will depend on the genetics and the environmental factors so, it is very important to have a healthy lifestyle that will keep a healthy gut.

You can take care of your gut health and even repair it by eating healthy foods such as fruits, vegetables, antioxidants, bone broth, prebiotics (high fiber food such as lentils, green peas, blueberries and strawberries) and probiotics (fermented foods such as yogurt and pickles) to keep a healthy microbiota in the gut.

In other words, you want to have good bacteria in your gut to keep a healthy intestine wall lining that can protect you from bad bacteria and other microorganisms and toxins. In some cases, it would be useful to take digestive enzymes to help break down the food particles so that, they can be properly abdorbed in the intestine wall. Collagen and L-glutamine might be useful to help repair the intestine wall lining. Remember to exercise and also, to get enough hours of sleep every night and enjoy life to live a healthier and happier life.

Finding the root of what is causing the chronic inflammation and solving it will allow you to heal faster.

To know where you can find more information about how the gut might be related to chronic inflammation and autoimmune disorders, read my article about the IBS and SIBO Summit and the Autoimmune Summit.

If you have any comments, please, leave them in the section below.

Your friend,

Dr. Verónica Giannoni


  1. S. Manfredo Vieira, M. Hiltensperger, V. Kumar, D. Zegarra-Ruiz, C. Dehner, N. Khan, F. R. C. Costa, E. Tiniakou, T. Greiling, W. Ruff, A. Barbieri, C. Kriegel, S. S. Mehta, J. R. Knight, D. Jain, A. L. Goodman, M. A. Kriegel. Translocation of a gut pathobiont drives autoimmunity in mice and humans. Science, 2018,; 359 (6380): 1156 DOI:10.1126/science.aar7201
  2. Yale University. “The enemy within: Gut bacteria drive autoimmune disease.” ScienceDaily. ScienceDaily, 8 March 2018,. <www.sciencedaily.com/releases/2018,/03/180308143102.htm>.

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