How To Improve Gut Health & Digestion With Autoimmune

anti-inflammatory digestion stress Apr 08, 2023

Hippocrates said, “All disease begins in the gut.” Why is that and what does that mean for those of use with autoimmunity?

Nausea, heartburn, indigestion, upset stomach and other bathroom woes are common when taking medication or living with an autoimmune, and red flags that the digestive tract needs some attention. This is because medication, food sensitivities, movement and stress hormones can all interfere with digestive function and increase contributing factors for inflammation elsewhere in the body. 

For example, acid blockers interfere with the production of stomach acid needed to help breakdown protein and kills bacteria passing through the body. NSAIDS can contribute to ulcers and perforation of intestines. Steroids, antibiotics and birth control can give rise to yeast & bacterial overgrowth. Stress depletes acids and enzymes needed to break down food, and will reroute blood and nutrients from the digestive to other ares of the body.

If improving symptoms of inflammation, energy or metabolism with autoimmune is a goal, looking at and improving the role of “gut health” and digestive function in overall health is a must-do. 

This is why Digestive Function is included in The Autoimmune Nutrition Triad and everything I do with my private clients and members inside The Integrative Autoimmune Network.

Restoring gut or digestive wellness starts by understanding why digestive function is important to your health goals, and some first steps to help address potential imbalances that may be impacting symptoms.

This article explains: 

  • Why “gut health” and digestion are important to reducing inflammation with autoimmune
  • What causes leaky gut
  • Signs and symptoms of leaky gut
  • How to improve digestion 
  • Food and lifestyles considerations


Why is gut health important for autoimmune?


The gut’s main role is to act as a barrier – to let things in that are beneficial and to keep things out that are detrimental to health. It allows us to absorb the nutrients we need to stay healthy and to eliminate waste. This seemingly simple role is actually quite complex and the system can break down in many places.

For one thing, our guts can "leak." Yes like a long tube with holes in it or a brick wall that has lost some mortar, it can allow things to get into our bloodstreams that can cause imbalances and trouble elsewhere. 

This is called “intestinal permeability” of the epithelial lining in the intestines.


What causes leaky gut with autoimmune?


Pro-inflammatory foods, antibiotics, medications, chemicals, chronic perceived stress, excessive intensive exercise, no movement and bacterial imbalances (opportunistic or pathogenic microorganisms from travel, pets or having inadequate beneficial bacteria) in the intestinal tract can all damage the epithelial lining, allowing foreign antigens (antagonists) to enter the bloodstream.  

When foreign antigens enter the bloodstream (and if a person is predisposed), they can cause an inflammatory or autoimmune response such as joint/muscle pains, headaches, migraines, irritable bowel, chronic sinusitis, fatigue, thyroid, food allergies/sensitivities, the list goes on ….

There is some debate as to what exactly is “leaking” into the blood system: bacteria, gasses from bacterial overgrowth (endotoxins, mycotoxins, aldehydes) or protein fragments from bacteria themselves, undigested food proteins or toxins. 

The verdict is still out, but we do know there is intestinal inflammation and a trigger of some sort that can start an autoimmune cascade. 

Research around gut health and autoimmunity could be one of the most significant medical health advancements of our time. The integrative community is thrilled as gut health is always discussed first and foremost with clients and has been done so for centuries.


Inflammation and autoimmunity


We all know that inflammation drives disease. But what drives inflammation? Physical stress (issues in tissues) and perceived or mental stress (lifeload, stranger danger). The body can’t tell the difference. 

Leaky gut or imbalances in the digestive tract is a form of inflammation or physical stressors in the digestive tract and it’s incredibly important to those with autoimmunity.

Why? About 70% of our immune system lives in or around our gut - in the intestinal linings and lymphoid tissues that surrounds the digestive tract where B-Cells and T-Cells are produced, just like the spleen. 

So, if the digestive system is inflamed, if gasses, proteins or whatnot are permeating the intestinal lining, entering the bloodstream and/or interacting with the lymphoid tissues that sits around this system, the immune system can become triggered, driving symptoms. 

For example, some studies show that RA, JIA, gout and ankylosing spondylitis patients had abnormalities and less diversity in their gut microbes, 62% of those with an inflammatory bowel disease (IBD) have rheumatic symptoms - this is called peripheral arthritis and visa versa ... psoriatic arthritis, ankylosing spondylitis and reactive arthritis are types of IBD-associated arthritis.

So, a key part of getting autoimmunity-related symptoms under control means working to improve gut or digestive health and function. 

This includes ensuring you have a good balance of good bacteria in your intestines … Microbes that help digest and absorb nutrients, fight off opportunistic, pathogenic or disease-causing microbes, make some vitamins for us, and have all kinds of other health benefits, like mental health, reducing inflammation and stabilizing blood sugar.


Signs and symptoms of leaky gut


There are many indicators of digestive imbalances or leaky gut. None of these symptoms are proven to directly cause leaky gut (we discussed possible causes above). However, intestinal permeability is commonly present in many of these conditions:

  • Adrenal fatigue
  • Allergies and food sensitivities
  • Autoimmune disease (lupus, MS, RA, type1 diabetes, Hashimoto's, and more)
  • Autism
  • Candida
  • Chronic fatigue syndrome
  • Chronic inflammatory conditions (arthritis)
  • Celiac disease
  • Inflammatory bowel disease (Crohn’s, Colitis)
  • Irritable bowel syndrome
  • Diarrhea
  • Gastric ulcers
  • Inflammatory skin conditions (eczema, psoriasis)
  • Obesity-related complications (type 2 diabetes, fatty liver, heart disease)
  • Small intestinal bowel overgrowth (SIBO)
  • Thyroid disorders
  • Parkinsons
  • Propensity to gain weight, despite a balanced diet and exercise
  • Nutritional deficiencies (ridges in nails is a good indicator, anemia despite eating recommended amounts of iron)


How to improve gut health

There are a lot of natural ways to improve gut health. Let’s focus on two first steps as these can make a substantial shift and these are things within your control. Most people require professional guidance at some point in this journey to make changes that stick, but there is a lot you can do to get started.


STEP ONE: You are what you eat

Food is 80% of the solution when it comes to restoring digestive imbalances and addressing leaky gut because when we have autoimmune, we need to eat in a slightly different way than someone who does not to help us reign in our hyper immune response. 

It’s always best to identify and eliminate the cause, so, let's stop giving our guts junk. Try eliminating added sugars, processed foods, and alcohol for a few weeks. You will be amazed at how much better your body (and gut) feels with this first step.

If you have already done this, you can go one step further and identify your unique food triggers. 

Food triggers will vary from person to person, but common ones for autoimmune include: 

  • Dairy and grains (gluten and non gluten) contain common compounds known to irritate the gut lining
  • Eggs are one of the more common food allergens and are particularly good at getting into cells for immune reactions
  • Soy, corn and sugar beets are hidden in so many processed foods and highly genetically modified, as well as sprayed
  • Seeds, nuts, legumes and nightshades may also be triggering for some, but not all
  • Some are also extremely sensitive to fungicides and other sprays used on crops

What you add to your plate is equally important to restoring gut health.  Protein, fats and fiber are essential. 

Fiber in particular plays lots of roles in our gut, including whisking away bacterial fragments and toxins so they can be eliminated. It binds and removes excess cholesterol and hormones. Fiber also helps to feed our friendly resident microbes that help us absorb and digest our food better.

What foods have a lot of fiber?

Fruits, vegetables, nuts, seeds, avocado and even cacao. If you can't get your required 10 servings of fruits/vegetables daily, I often recommend a fiber supplement like a couple tablespoons of ground flax or chia seeds daily. And if you have an IBD that is flaring, focusing on cooked foods may be helpful vs. raw.

Helping clients identify their unique triggers for flares and embrace an easy-to-follow autoimmune-friendly diet is exactly how I serve clients. You can learn more about that here >>> Food Freedom 


STEP TWO: Lifestyle factors for better gut health

Inflammation is caused by stress and stress can be both physical (issues in tissues) or perceived (lifeload). The body can’t tell the difference between either “threat” and will initiate the same hormonal response to help the body prioritize critical actions and processes to deal with the threat at hand.

During that stress hormone response (designed to protect the body), one of the messages and actions is to “suppress digestive function” (less blood flow and nutrients to the GI tract). This is done to divert and conserve resources for other actions to “deal with the threat” (wherever that is). 

This explains in part why so many people who are trying to “eat clean” don’t experience the relief they want with dietary changes alone when they also have a large lifeload or career. And the link between IBS and anxiety.

Work. Aging parents. Kids. Social situations. Traffic. Over exercise. Not enough exercise. Ruminating thoughts. Worrying.

In fact, I see this a lot with my clients who are teachers, healthcare providers, lawyers, accountants, office managers, entrepreneurs and c-suite execs. 

Getting lifestyle influences - and response to lifeload stressors - under control is an essential part of improving digestion, especially when you can’t change your circumstances or when changes to food seem hard.

Two easy lifestyle factors that I recommend to all my clients to promote good gut health AND improve how the body responds to “stressors” on a physical level are breathwork and mindful yoga. 

These two disciplines have a huge body of research behind them that shows they can improve how the body metabolizes both physical and perceived stressors, in some cases in as little as 10 minutes! 

In fact, I believe in these two disciplines so much that I created an entire membership around them (also including nutrition) because my clients were desperate to find something effective and suitable for their busy lives, AND also honoured their physical restrictions. 

The beautiful part of both breathwork and mindful yoga is that any BODY can embrace these modalities. They are also scientifically recognized by both medical and research communities as having profound impact not only on digestion, but immune, mental and hormonal health. 

You can learn more about a whole body approach for digestive wellness that includes autoimmune nutrition, breathwork and mindful yoga here >>> The Network



  • Leaky gut or bacterial imbalances is common with autoimmune due to medications, inflammation, and lifestyle influences
  • The function of your gut or digestive tract is critical to getting autoimmune symptoms under control 
  • There are many signs and symptoms of poor digestive function, and these should be taken seriously
  • Identifying food sensitivities is a key part of improving digestive function along with increasing the nutritional value of what we’re eating, including fiber
  • Eliminating common gut irritants like added sugar, processed foods, and alcohol is a good first step to help improve gut health.
  • Sticking with nutrient-dense unprocessed foods is always a good plan, whether you have gut issues, other concerns, or feel completely healthy
  • Increasing fibre by means of fruits, vegetables, seeds and nuts will help improve digestive health
  • Digestive imbalances are not always caused by food and lifestyle changes can also have a major impact on digestive wellness




Sign Up For My Next Masterclass

Anti-Inflammatory Weight Loss For Autoimmune

Click Here For Details