bacteria that cause autoimmune disease

14 Gut Bacteria That Cause Autoimmune Disease

Do you live in Ottawa? Are you looking to find out the gut bacteria that cause autoimmune disease?

If so, you are in the right place.

Today, I will discuss microbiome dysbiosis and autoimmunity and list the 14 gut bacteria that cause autoimmune disease.

Even better, I will give you some guidelines on how to treat dysbiosis naturally.

In this Article:

Let’s jump in and look at the incidence of immune disorders.

What is the incidence of Immune Disorders?

Since the middle of the last century, Immune Disorders, including Autoimmune diseases, have rapidly risen.

For example, Multiple Sclerosis has increased by 300% since 1950. 

Crohn’s disease has increased by 400% since the mid-1950s.

Type 1 Diabetes has risen by 300% since the 1970s.

One out of 2 Americans in the US suffers from an immune disorder, with 53 million having an Autoimmune disease. 

Additionally, over two million Canadians are estimated to be affected by autoimmune diseases.

So, why has this rapid increase?

Genetics could play some role, but they take much longer to change.

Recently, researchers have been looking at the role of the gut microbiota and autoimmunity. 

In a review paper, a researcher, Yehuda Shoenfeld, described the Microbiota as the “crossroads of autoimmunity.”

Let’s look next at what we mean by the Microbiota.

What Is the Microbiota?

The Microbiota consists of various microbes (bacteria, fungi and protozoa), genes, proteins, and metabolites.

If these enter our bloodstream, they cause severe health risks, including developing autoimmune diseases.

Researchers illustrated this idea excellently in a mouse study that introduced a bacteria that triggered the development of Crohn’s Disease. They later gave the mouse a bacteria that activated the immune system to put Crohn’s into remission.

Although this was a mouse study, it is relevant to human physiology.

Let’s look next at what disorders are associated with an imbalance of the Microbiota or dybiosis.

What Disorders Are Associated With An Imbalance Of The Microbiota?

An imbalance of the Microbiota or dybiosis is associated with various autoimmune and immune disorders, including the following:

  • Inflammatory Bowel Disease
  • Irritable Bowel Disease
  • Celiac Disease
  • Cystic Fibrosis
  • Chronic Fatigue Syndrome
  • Acne
  • Eczema
  • Psoriasis
  • Urticaria
  • Autism
  • Childhood hyperactivity
  • Pancreatic Insufficiency
  • Weight gain
  • Gallbladder dysfunction
  • Environmental illness

Furthermore, several studies examine the Microbiota composition in specific conditions, including Autism, Lupus, and Rheumatoid Arthritis.

To help us understand the composition of the Microbiota, the development of more sensitive stool testing has come a long way in the last ten years.

The Development Of Stool Testing

Stool testing in the past used culture technology, while today, the most sensitive stool tests use Quantitative PCR (qPCR) technology.

Conversely, qPCR testing looks at the bacteria’s genome in the stool, which allows us to measure both type and quantity of bacteria present.

Also, qPCR testing looks at pathogenic microbes and bacteria associated with specific autoimmune conditions.

Such a test is the GI Map Test by Diagnostic Solutions, which is available to health practitioners.

Let’s look next at what microbes are associated with specific autoimmune conditions.

What Bacteria Cause Autoimmune Disease?

Below is a list of GI microbes and their associated autoimmune disorders:

  • Klebsiella – Ankylosing Spondylitis
  • Citrobacter, Klebsiella, Proteus, Prevotella – Rheumatoid Arthritis (RA)
  • Bacteroidetes supp – Arthritis in general
  • Fusobacterium – Systemic Sclerosis
  • Mycobacteria – Psoriasis and Crohn’s
  • Yersinia – Grave’s and Hashimoto’s
  • Streptococcus – Pandas
  • Chlamydia, Salmonella, Shigella, Yersinia – Reactive Arthritis
  • S.Pyogenes – Rheumatic Fever
  • Campylobacter jejuni – Gullian Barre Syndrome
  • E.coli, Proteus – Autoimmunity in general

Importantly if you have any of the above bacteria in a stool test result, that doesn’t necessarily mean you will develop the associated condition.

A disease is determined by various other factors, such as genetic predisposition if you develop.

Let’s look at microbes cause autoimmunity.

How Do Bacteria Cause Autoimmunity?

Like food, antigen microbes initiate autoimmunity by triggering the immune system to become confused between peptides on the surface of the bacteria and other similar peptides in the body.

The body’s immune cells then begin to attack the host’s tissue.

In addition to this, we find bacteria throughout the GI tract, including the mouth.

Let’s look next at an example of a bacteria association with an autoimmune disease.

Oral Bacteria and Autoimmune Diseases

An infectious oral microbe known as Porphromonas gingivalis is a primary cause of Periodontal disease or Gingivitis.

This microbe produces peptidyl arginine deiminase 4 (PAD4), an enzyme that mediates proteins that cause RA.

Stealth Infections And Autoimmunity

Similarly, RA is associated with a stealth infection called Proteus, which we predominately found in the bladder, especially in women.

Interestingly women with RA have a higher predominance of urinary tract infections.

Orthodox treatment of Proteus is with strong antibiotics such as Cipro.

An alternative is a Silver supplement such as Silverpure Liquid, a potent antimicrobial without the side effects of antibiotics.

Silver is an effective agent against other resistant microbes, such as E.coli, MRSA and Enterococcus.

Let’s look now at how microbes can lead to Thyroid autoimmunity.

Yersinia and Thyroid Autoimmunity

If Yersina overgrows in the gut, it can lead to autoimmunity towards the TSH receptors on the thyroid. The Yersinia marker is on the GI Map test.

Now we have identified the 14 gut bacteria that cause autoimmune disease let’s look at how we can treat them.

How Can We Treat These Microbial Overgrowths/Dybiosis?

You can treat dysbiosis using antibiotics such as Refaximin, but they tend only to help when being used.

Herbal Antimicrobial supplements, Oil of Oregano, and probiotics also work but are often better than antibiotics.

It would help if you also looked at the effect of food sensitivities on autoimmunity.

Food Sensitivity and Autoimmunity

People with Celiac disease have approximately ten times the risk of developing autoimmune thyroid diseases like Graves and Hashimoto’s.

So, it is essential to consider the removal of gluten from people with thyroid autoimmunity.

There is a marker for gluten sensitivity on the GI Map test.

Also, you may consider removing Milk proteins, which can trigger autoimmunity like Type 1 Diabetes.

Leaky Gut and Autoimmunity

Leaky gut or intestinal permeability is another crucial driver in the development of autoimmunity.

Various factors, such as inflammation along the gut lining from dybiosis, cause a leaky gut.

Once the inflammation is under control, some supplements can aid in healing the gut lining, including GI Revive.

Some Good News

Good-quality Chocolate and Coffee have a protective effect against the development of autoimmunity.

Now It’s Over To You

Do you have an autoimmune disease?

Have you considered looking at whether you have microbiome dysbiosis?

Leave me a comment below.

Do You Need Help?

If you need help, I suggest you book a free functional medicine discovery session with me to determine whether my approach fits your toddler’s needs.


The information provided on this website is for educational purposes only and is not intended to diagnose or treat any disease. Please do not apply this information without first speaking with your doctor.

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