Why Your Healing Begins in the Gut

autoimmune disease blog leaky gut rheumatoid arthritis healing Feb 26, 2019

In the previous article, I mentioned that there were three causes of autoimmune disease: genetics, environmental triggers and food/lifestyle.  

Your genetics determine what illness you may be predisposed to, your weak link,  but your genes don’t cause the illness to be triggered.  The combination of environment, food and lifestyle can create a cascade of problems in the gut.  Yes, autoimmune disease is actually a gut health issue!  This is why your healing begins in the gut. 

Autoimmune disease is actually a gut health issue

That blew my mind!  My joint pain was actually due to problems in my gut.  Who knew?

Through my research I discovered that every person with autoimmune disease who has been tested, including rheumatoid arthritis, has a condition called leaky gut, or intestinal permeability. In fact even people without an autoimmune condition can have leaky gut.

What is leaky gut?

To understand leaky gut, we first need to learn a little bit about digestion.  Most digestion takes place in the small intestine, the middle coiled up section in the diagram below. The small intestine is lined with villi, like fingers, which absorb nutrients, giving the small intestine a huge surface area for absorption. The villi have a single cell membrane to keep the digestive tract separated from the inside of the body. 

This membrane has special channels called tight junctions which allow just the smallest molecules into the body. If the membrane becomes damaged, then absorption is reduced. As well, larger molecules can get through damaged tight junctions. 

About 70% of your immune system is in the gut.  It is always on patrol, just inside membrane, on the lookout for bad guys.  When the bad guys get through the membrane, the immune system goes on high alert as it tries to deal with these foreign invaders. Sometimes it gets confused since some of these invaders look very similar to our own body tissue. 

Next thing, the immune system is attacking our own body tissue.  In the case of rheumatoid arthritis, it’s the synovial lining around the joints.  For psoriasis, it's the skin.  For celiac disease it’s the gut lining itself.  So the tissue which gets attacked depends on your genetics, but it begins with leaky gut. Therefore, your healing begins in the gut too!

What causes leaky gut?

It may be easier to understand how to heal leaky gut if we first look at what causes leaky gut.  Leaky gut is essentially caused by environmental, food and lifestyle factors.  In this blog I talked about the causes of rheumatoid arthritis and guess what? The causes of leaky gut are the same: environmental exposures, food and lifestyle.  Here is a list of common contributors to leaky gut:

  • Food sensitivities: alcohol, grains, dairy, eggs, GMOs, nightshade vegetables, sugar

  • Exposure to toxins

  • Gut infections: parasites, bacterial overgrowths, yeast overgrowths.

  • Medications: acid blocking medications, antibiotics, birth control pills, NSAIDS, prednisone

  • Exposure to molds 

  • Chemotherapy

  • Radiation

  • Physical stress

  • Emotional stress 

  • Surgeries 

Usually several of these factors combine to cause the digestive system to not function optimally.  Living in our digestive tracts along with our own cells are bacteria and other microorganisms collectively called the microbiome. Our bodies have evolved with these organisms and we couldn’t live without them.


When we are exposed to one or more of the leaky gut contributing factors listed above, the microbiome can get disrupted, or out of balance, a condition called dysbiosis.  This results in an overgrowth of the wrong kind of bacteria or the right bacteria living in the wrong place. This may become obvious to you with signs of digestive distress, like:

  • acid reflux

  • heartburn

  • burping

  • gas

  • bloating

  • cramps

  • constipation

  • diarrhea

  • irregular bowel movements

  • undigested particles in the stool

Sometimes, however, there may not be apparent problems with digestion.

Other symptoms of leaky gut include issues with:

  • Respiration: allergies, asthma, congestion, chronic coughing, congestion, 

  • Skin: acne, rashes, rosacea, eczema 

  • Joint and muscles: pain and inflammation 

  • Brain health: brain fog, depression, anxiety, dizziness, frequent headaches, mood swings, ADD/ADHD 

  • Hormones: imbalances, irregular periods, PMS, perimenopausal symptoms

  • Other: fatigue, insomnia, low white cell blood count, weight gain or the inability to lose weight, infertility, thyroid imbalance

Also very surprising and disheartening is that many of the medications used to treat rheumatoid arthritis and other autoimmune disease CONTRIBUTE to leaky gut.  How very frustrating for people who are already ill to know that the medications prescribed to them, while they may suppress symptoms temporarily, actually make the underlying cause WORSE!  

I must stress that I am not endorsing going off medications!  You can begin your healing in the gut and become healthier while on medications. Work with your practitioner on this. 

There are many physicians who still believe that the food you eat does not play a role in your autoimmune disease.  There is so much evidence to the contrary now that this is simply not true.  It will just take a while for conventional medicine to make the required shift.  

Meanwhile functional medicine does address root causes and the focus with functional medicine practitioners (and health coaches!) is on healing the gut. 

Heal Thy Gut!

If you are feeling frustrated and angry about what you just read, there is hope.  It IS possible to heal your gut!  Many people, including me, have done exactly that.  This is good news and there is HOPE!  One of the best things is that healing the gut begins with you.  YOU can control your environment and the food you eat.  

In upcoming blogs, I will delve into how your healing begins in the gut.  I will tell you that it requires food and lifestyle changes.  These changes aren’t necessarily easy, but freedom from pain and being controlled by your illness definitely is worth the effort!



References used in this blog:

Ballantyne, S., (2013) The Paleo Approach: Reverse Autoimmune Disease and Heal Your Body, Victory Belt Publishing

Myers, A., (2017) The Autoimmune Solution: Prevent and Reverse the Full Spectrum of Inflammatory Symptoms and Diseases, HarperCollins Publishers


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  2. All information in this post is based on my personal experiences. Please discuss any changes to your diet with your healthcare team. No information in this article is meant to replace medical advice. Please read my Terms and Conditions.