Autoimmune Digestive Diseases & The Gut Microbiome

by | May 11, 2021 | Chronic Illness, Digestive Health, Naturopathy, Nutrition

Autoimmune diseases are on the rise.

What are autoimmune diseases?

Autoimmune diseases are when the body mistakes it’s own tissue for an invader/pathogen, and mounts an attack. When this becomes chronic, chronic immune activation causes inflammation and  damage to the issues, creating a disease state.

The are two main branches of teh immune system: innate immunity and adaptive immunity.

Innate immunity: your innate immune system is the immune system functioning you were born with, and includes mucous membranes such as your nasal passages, lungs and gut. These barriers keep harmful substances and microbes from entering your body. Lining these passageways are immune molecules such as lymphocytes, macrophages and white blood cells. These cells monitor the state of your body on an ongoing basis, to protect you.

Adaptive immunity: the response your body mounts in order to defend itself against a pathogen, such as a virus or bacteria. This can trigger the release of inflammatory immune molecules called cytokines, that often create chronic inflammation.

Autoimmune diseases are diseases of the adaptive immune system. 

Many autoimmune diseases are linked to the gut microbiome, especially gastrointestinal autoimmune conditions such as Celiac Disease and IBD (Crohn’s and colitis).

Typically, it’s the combination of genetics + chronic stress + trigger (such as childbirth or gut bacteria) that triggers the onset of an autoimmune digestive condition.

It’s important to know that having one autoimmune disease, such as Celiac disease, puts you at risk of developing other autoimmune diseases.

What’s the connection between the gut microbiome and autoimmune diseases?


Your gut bacteria interact directly with your immune system – up to 70% of which is in your digestive tract.

When your gut bacteria become imbalanced due to poor diet, stress, medications, this imbalance can allow inflammatory bacteria and other microbes to take over.

Healthy bacteria help modulate a healthy immune response in the gut.

The microbes interact with the immune system via through the intestinal lining, and interact with the immune system by triggering the release of immune molecules called cytokines which can be either inflammatory and anti-inflammatory.

When you have a microbe imbalance in your gut, your body mounts an immune response to the inflammatory bacteria, in an attempt to kill the bacteria and restore balance in the gut.

This chronic immune activation and inflammation eventually results in your body mistaking your own intestinal cells for invaders, and your body starts to mount an attack on your own intestinal cells – this is an autoimmune response, which can eventually result in a full blown autoimmune disease such as Celiac or IBD – Crohn’s disease or colitis.


Small intestinal bacterial overgrowth (SIBO) is increasingly common, and increases the risk of small intestine autoimmune disease including Celiac Disease and Crohn’s.

SIBO can develop from a variety of factors including:

  • low stomach acid
  • use of antibiotics and antacids
  • poor diet
  • chronic stress
  • chronic constipation
  • trauma: concussions, other physical or mental emotional trauma
  • abdominal surgery
  • other health conditions such as Celiac disease or Hashimoto’s

In both diseases there is an underlying gut bacteria imbalance.

sibo small intestine autoimmune gastrointestinal disease IBD celiac

Why does small intestine inflammation matter?

Your small intestine is the site of absorption for your food.

It’s lined with tiny hairs called cilia which help to absorb nutrients, and the gut lining also produces digestive enzymes to break down and help you absorb your food.

When the cells of the small intestine become damaged you can no longer properly digest or absorb your food which can result in malabsorption, bowel symptoms and a number of nutrient deficiencies including vitamins D, A, E, B12, iron and more.

*see the image for comparison of healthy versus damaged cilia.


General sign & symptoms of autoimmune digestive diseases

  • chronic diarrhea or constipation
  • early fullness: feeling small after only a few bites of food
  • chronic indigestion & bloating
  • food reactions/sensitivities
  • chronic bloating
  • unintentional weight loss
  • chronic fatigue (due to inflammation and malabsorption)
  • skin conditions: atopic dermatitis, eczema, rashes, psoirasis, rosacea
  • frequent illness


    Chronic small intestine inflammation can damage cilia and enzyme production, leading to malabsoprtion and nutrient deficiencies.

    small intestine SIBO gastrointestinal autoimmune disease IBD celiac

    Risk Factors for Digestive Autoimmune Conditions

    It’s more than just genetics, there are several risk factors that make someone more likely to develop Celiac, Crohn’s or Colitis.

    • SIBO: small intestine bacterial overgrowth
    • Genetics: a close relative with Celiac Disease or other autoimmune disease
    • Food poisoning or other bowel infection
    • Viral illness/post viral syndrome



    Left untreated, digestive autoimmune diseases can cause a wide variety of multi-system health issues and complications including:

    • Development of other autoimmune diseases such as autoimmune hypothyroidism or autoimmune hepatitis
    • Chronic digestive issues and conditions: heartburn and indigestion, gallbladder malfunction, pancreatic insufficiency
    • Malabsorption and nutrient deficiencies: all macronutrients
    • Mental health issues: new or worsening of pre-existing
    • Weight loss and muscle wasting
    • Chronic fatigue
    • Nervous system disorders
    • Dermatitis
    • Anemia
    • Osteoporosis
    • Low mood and mental health disorders
    • Chronic pain
    • Insomnia

    Treatment of Autoimmune Gastrointestinal Diseases


    A naturopathic approach to treating any illness to to address the root cause(s).

    Common root causes include:

    • genetics
    • dysbiosis: gut bacteria imbalance
    • infections
    • chronic stress and adrenal fatigue (aka “burnout”)

    A naturopathic treatment plan would include:


    Finding and treating the root cause(s) of the inflammation: this may involve various testing including stool tests.

    At Verdure, we offer a variety of stool tests that provide detailed information for your practitioner to build an effective, and science-based personalized healing plan that addresses the underlying causes of your digestive concerns.

    The most commonly used test is called the GI MAP, which is a comprehensive PCR stool test.

    This test measures:

    • types of bacteria, parasites, viruses and yeasts and their relative amounts
    • bacteria known to trigger autoimmune conditions
    • markers of inflammation
    • markers of digestion

    Learn more about the GI MAP test here.


    Your personalized gut healing plan

    Once your practitioner receives your test results, they build a a personalized, 4R gut healing protocol to treating any underlying dysbiosis or SIBO to reduce inflammation and improve absorption.

    Dietary changes: avoiding sensitivities, easy to digest, nutrient-dense foods

    Stress management & lifestyle changes: setting boundaries, slowing down, prioritzing rest, mindset shifts


    Your practitioner will prescribe a personalized supplement protocol based on your needs, including supplements to restore nutrient deficiencies, optimize digestion, reduce inflammation and modulate the immune system.



    Concerned you may have an autoimmune condition?

    Diagnosed, but still struggling with symptoms?

    Book an appointment with naturopath Dr. Stacy Burke, ND.

    Verdure Wellness Clinic in Waterloo, ON offers naturopathic medicine, acupuncture, nutrition consulting, massage therapy and chiropractic care. Our team of health practitioners offer a variety of services with your best health and wellness in mind.

    305-55 Erb Street E, Waterloo, Ontario   •    519.742.0691

    [email protected]    •    BOOK NOW   •    ABOUT   •    CONNECT

    Pin It on Pinterest