What does the gut have to do with joint pain, fatigue, thyroid imbalance, psoriasis and a host of other autoimmune diseases and symptoms?

It turns out, a lot!

The latest research on autoimmune disease tells us that it may start in the gutWe are learning that the bacteria that live in our gut have an important influence on the immune system, inflammation, and even our mood.



The Microbiome


The bacteria that reside mainly in our large intestine are referred to as the microbiome. This is a delicate ecosystem that exists in a symbiotic relationship with human cells. In fact, bacterial cells outnumbers our own human cells 10-fold!

It’s no wonder that the microbiome has become the focus of research on human health in the past few years. The results of this research are fascinating!

We now know that these bacteria are influenced by the environment we surround them in.

The environment can lead to competition between “good” and “bad” types of bacteria. The food that we eat can influence whether the good or bad bacteria thrive. In general, we know that sugar feeds harmful bacteria, while FIBRE (aka fruits and vegetables) feeds beneficial bacteria.

Food isn’t the only factor; lifestyle and genetics plays a role in what our bacteria look like. Bacteria respond to our stress, water intake, sleep, exercise, and many other factors.

So, how does this all relate to autoimmune disease?

Science indicates that autoimmune conditions may result from an imbalance in the human-microbiome relationship. Human and bacterial cells exist in a delicate balance and, when disturbed, symptoms of chronic disease can develop.

While some of the circumstances that tip this balance may be out of our control (i.e. genes, pollution, pesticides, antibiotics), we can influence the nutrients that the beneficial bacteria need to thrive.

Our genes are fixed at birth, but our microbiome is not. This is where holistic nutrition comes into play.



Nutrition and Microbiome Support


Our bacteria are alive and need to eat! Nutrition can help to support our bacteria in a number of ways. You may have heard of probiotics and prebiotics before, so what are they all about?


Probiotics vs. Prebiotics: What’s the difference?


Essentially, probiotics are actual bacteria that can live for a limited period of time in our digestive track (large intestine mostly). Prebiotics are the indigestible fibres that our bacteria eat. Essentially, prebiotics feed the probiotics!


To optimize the health of your microbiome, you should be eating prebiotic foods
when taking probiotic supplements.


You can increase the presence of good bacteria, reduce inflammation, support the immune system and reduce gastrointestinal issues by including both pre- and pro-biotics in your nutrition protocol. You can think of prebiotics as fertilizing the good bacteria, allowing them to flourish, while preventing the bad and disease-causing bacteria to thrive.

Prebiotics are usually indigestible fibres that bypass digestion in the small intestine. Once they reach the large intestine, they ferment into short-chain-fatty-acids which protect the gut lining and provide food for the good bacteria that reside there.


Benefits of Prebiotics:
  • reduce constipation
  • increase energy
  • repair the gut lining (i.e. reduce ‘leaky gut’)
  • increase immune function
  • increase vitamin production
  • increase calcium absorption and bone density
  • regulate weight management
  • reduce dysbiosis of the microbiome


Prebiotic-rich food:
  • garlic
  • onions
  • apples
  • bananas
  • Jerusalem artichoke
  • asparagus
  • beans
  • jicama
  • leeks
  • yam
  • chicory root
  • dandelion


Probiotics are the live and healthy bacteria that reside in our gut. We can increase our intake of probiotics through eating fermented foods or supplementing with them directly.

Probiotics in supplement form do not recolonize our microbiome when we loose diversity, but they can take up space to prevent harmful bacteria from flourishing. In order to recolonize lost strains, fecal microbiota transplant is needed, which is not yet approved for autoimmune disease.

There are several strains of bacteria that are known to be beneficial for reducing inflammation, supporting the immune system, and maintaining general health of the microbiome. Probiotic strains typically include various species of the genera Lactobacillus and Bifidobacteria.

Probiotic supplements are considered a Food or Natural Health Product in Canada. One way to determine which strain(s) and product may be best for your condition, is to consult this Canadian guideline for probiotic products. You should also choose a supplement in consultation with your healthcare provider.

Although the research is still in it’s infancy, probiotics can have a positive effect on autoimmune health.


Benefits of Probiotics:
  • improve digestion
  • reduce constipation
  • reduce inflammation
  • strengthen the bowel wall
  • increase mineral absorption
  • regulate hormone production


Fermented Foods: Traditional ways of feeding our microbiome


Before probiotic supplements, there were fermented foods. As an archaeologist, I’m fascinated by the ways that humans consumed probiotics through the use of fermentation. Some of the earliest evidence of fermentation techniques date back to over 9000 years ago!

Today, popular fermented products include dairy, kefir, sauerkraut, kimchi, pickles, miso, tempeh, and drinks such as kombucha. These probiotic-rich foods have made a come-back in the last decade and for good reason! The standard North American diet and increased exposure to antibiotics has, in general, reduced our microbiome diversity.

We can begin to reverse this trend by incorporating more pre- and pro-biotics into our daily nutrition habits. Fermented foods can also help us digest our meals because they contain natural digestive enzymes. These help to break down food into nutrients we need to thrive. They’re also a great way to decrease sugar cravings.

If you’re new to fermented foods, start slowly. They change the balance of the microbiome, which can lead to some initial intestinal discomfort. Record changes to your digestion and adjust your intake as needed. Working with a nutritionist can be beneficial during this introductory phase.


How to Optimize The Microbiome


Putting all of the pieces together, supporting our microbiome health comes down to some key ingredients:


  • decreasing stress
  • supporting digestion
  • regulating sleep
  • increasing prebiotic intake
  • taking probiotics
  • eating fermented foods
  • eating quality, whole foods
  • reducing sugar intake
  • getting adequate exercise


If you struggle with any of the above, apply to work with me to create a personalized nutrition and lifestyle plan to support your microbiome and autoimmune health!


Our bodies are home to a complex and fascinating ecosystem of bacteria. We can utilize the power of holistic nutrition to restore balance and optimize health.


Gut health = Autoimmune health