I have spent two years, studying the work of experts in the field of autoimmunity and have combined what I’ve learned, in 24 steps.  I’ll be sharing one step every week for the next 24 weeks, on my website and social media platforms (starting Monday 18 May 2020).  This is step 15 of 24.

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We now know that three things must be present for an autoimmune condition to develop: a genetic predisposition, a leaky gut and a trigger.  (Thanks to research done by Alessio Fasano, MD in 2009) One of the triggers are infections.

According to Dr Amy Myers, the most common infections causing autoimmunity are candida overgrowth, small intestine bacterial overgrowth (SIBO) and intestinal parasites. Other infections like Epstein Barr (EBV), Herpes Simplex 1 and 2 (HSV) and E. coli have also been linked to autoimmune disease.

Epstein Barr is the infection that has been studied the most extensively in connection with autoimmune disease, and it has been linked to multiple sclerosis (MS), chronic fatigue syndrome, lupus, fibromyalgia, Graves’ disease, and Sjögren’s syndrome. According to Dr Amy Myers, 70% of healthy children test positive for EBV. In children with lupus, the rate of EBV infection is closer to 99%. 100% of people with MS test positive for EBV.

Viruses like EBV and HSV don’t leave your system. When your immune system is healthy, it keeps the viruses in check, but when it is suppressed by stress or illness, the infection can become active once again. Once the virus is active, your body’s immune response damages tissue, which then causes more inflammation and a bigger response from the immune system. Autoimmune disease develops from that chronic state of inflammation.


Candida is a fungus, which is a type of yeast. A small amount lives in your mouth and intestines. Its job is to help your body with digestion and nutrient absorption. When it is overproduced, it breaks down the wall of the intestine and enters the bloodstream, releasing toxic and other foreign invaders into your body and causing leaky gut.

Your gut microbiome is made up of good bacteria, bad bacteria and candida. Your good bacteria in your gut are supposed to keep your candida levels in balance. However, the candida population can get out of control as a result of the following:

  • Too many rounds of antibiotics, as antibiotics kill good bacteria.
  • A diet high in refined carbohydrates and sugar, which feed the candida. Fermented food might also feed active candida.
  • High alcohol intake, as it weakens your immune system.
  • Oral contraceptives.
  • Chronic stress as it weakens your immune system and shut down your digestive system.


Small Intestinal Bacterial Overgrowth or SIBO, occurs when the bacteria in your small intestine get out of balance and overgrow.

Most of your gut bacteria is meant to be located in your large intestine and colon, where they help to break down food, make vitamins and eliminate waste. When the good bacteria, that are normally found in the large intestine and colon, colonize the small intestine, SIBO occurs. SIBO can also be caused by an overgrowth of otherwise normal bacteria in the small intestine itself.

The excess bacteria then feed off of the undigested food in your small intestine. They love sugar, carbohydrates and alcohol. As the bacteria feeds, it causes the carbohydrates to ferment, which produces hydrogen as a byproduct. The hydrogen in turn feeds other organisms in your small intestine called archaea. The archaea then produce methane as a byproduct. So when you have SIBO you have high levels or hydrogen, methane, or both in your digestive system. Hydrogen-dominant SIBO typically leads to diarrhea, whereas methane-dominant SIBO leads to constipation.

In a healthy gut, bacteria gets passed through the digestive tract along with the food to the colon. There are a few possible reasons for this not to happen:

  • Damage to the nerves or muscles in the gut can result in leftover bacteria in the small intestine.
  • Physical obstructions in the gut, such as scarring from surgeries or Crohn’s disease, can cause an abnormal buildup of bacteria in the small intestine.
  • Tiny pouches can form in the wall of the small intestine and can collect bacteria instead of passing it on to the colon.
  • Some medications such as antibiotics, acid-blocking drugs, and steroids disrupt the balance of the gut bacteria.
  • A diet high in sugar, refined carbohydrates and alcohol.

Intestinal parasites

A parasite is an organism that lives on or in a host organism and gets its food from or at the expense of its host. Parasites can range from tiny organisms, visible only by microscope to several feet long tapeworms. They can enter the body through food, drink, contact with animals or infected people, or even just with skin contact.

Some parasites consume your food, leaving you hungry after every meal and unable to gain weight. Others feed off your red blood cells, causing anemia. Some lay eggs that can cause itching, irritability, and even insomnia. If you have tried to repair your gut and relieve your symptoms without any success, a parasite could be the underlying cause for many of your unresolved symptoms.

According to Dr Amy Myers,  theories behind how infections trigger autoimmunity are complex, and researchers are still trying to figure out the exact mechanisms.

Scientific theories on infections and autoimmunity

It is believed that infections can cause autoimmunity, make a condition worse or trigger a flare up. In her book “The Autoimmune Solution” Dr Amy Myers look at some of the theories scientists have come up with, to explain the link between infections and autoimmunity. Infections affect our immune system in multiple ways:

Molecular mimicry

Molecular mimicry happens when your immune system triggers an immune response to foods like gluten and dairy as well as certain cells in your body that have a similar molecular structure to gluten and dairy. Scientists belief that molecular mimicry can also be triggered by infections. If you have been infected with a virus or bacteria, your body might not be able to distinguish between the virus or bacteria and your own cells and start attacking both.

Casualties of war

According to this theory, if you have been infected with a virus or bacteria, your immune system rushes to the scene to attack the invader.  It attacks the infection but it also attacks your own tissue,  the innocent bystander or casualty of war.


This theory typically applies to Epstein Barr.  The Epstein Barr virus might highjack your cells’ DNA, trying to hide from your immune system by imitating your cells.  You immune system isn’t fooled and recognises the infection as an invader and triggers an attack on both the virus and the “highjacked” cells.

Our recommendation

Get tested for infections and work with a functional medicine practitioner to treat those infections.

To start your healing journey, I invite you to join the Autoimmune Way program today.  It’s a 6-month online course that gently guides you through each and every step of the healing journey.

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