10 most common causes of gut dysbiosis and how they can lead to autoimmunity

I'm Anindita!

I am a Functional Medicine certified Health Coach and AFMC Practitioner. I help women with autoimmune conditions I help women with autoimmune conditions reverse their symptoms with their body as their guide

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Did you know that having even one autoimmune condition makes you three times more likely to develop another? 

Or that 25% of patients with autoimmune diseases have a tendency to develop more than one condition?

I first came across this concept in the book “The autoimmune fix” by Dr Tom O’Brian.

At the time I was trying to find out as much as I could about eczema and anything related to immune health. I was desperate to help my daughter manage her severe eczema without having to be on strong medications for the rest of her life.

This book covered the important concepts of immune tolerance, immune dysregulation, and of course autoimmunity. This was just the beginning of my research on this topic. I went on to read many more research articles and books on this topic that helped to get a sense of which direction I needed to move towards.

This is how I found Functional Medicine which finally helped reverse her symptoms from within!

It all made so much sense!

This was my first reaction to reading this book.

At the same time, it was scary.

You see, getting a medical diagnosis for an autoimmune disease is only possible after significant tissue damage has occurred over years (and sometimes decades). But by then the damage is usually too severe and the medications that are given are mostly systemic drugs to suppress the entire immune system. This leads to a whole set of severe side effects.

We need to keep in mind that at times, these medications are life saving and necessary to stem further damage. But they are not the long term solution that we are looking for. These medicines are focused on symptom management.

On the other hand, the good news is that we get a window of opportunity to arrest the development of autoimmune diseases. And now we know enough about how to reverse this disease by restoring our body’s balance.

Functional Medicine is one modality that is particularly effective when it comes to complex, multifactorial diseases like autoimmune diseases. It approaches the human body as an interconnecting system and aims to address the root causes rather than medicating individual symptoms or even diseases.

The connection between your gut health and your immune system

In Functional Medicine, we look at the entire body and explore the interconnectedness at play.

80% of your immune system is your intestinal lining or your gut, which is why you need a healthy gut in order to have a healthy immune system.

Usually, we are told that autoimmune disease is only relevant and needs to be taken seriously when the specific auto-antibody markers are clinically high.

But that’s not really in our favour as we lose a precious opportunity to take preventive measures and prevent further damage.

Antibodies are produced as a protective mechanism by our immune system in reaction to some kind of trigger. If the level of exposure continues to increase, then the immune system continues to respond more and more aggressively. However, we may or may not feel this damage in the form of symptoms for a while.

And so the damage continues unabated along with the disease progression. If these antibodies are not clinically high to lead to a diagnosis, we are usually told that there’s nothing to worry about or that we need to look elsewhere in terms of identifying the causes.

And that’s not helpful either!

The spectrum of autoimmunity

There’s a whole shade of grey in between this black and white reality of having no autoimmune disease to being diagnosed with one.

This entire progressive state of disease is the spectrum of autoimmunity that has vibrant health at one end and degenerative disease at the other.

These progressive and different states will manifest in symptoms and various stages of tissue dysfunction at various places depending on genetic and other factors. This ongoing chronic, excessive inflammation will cause cellular damage, then tissue damage and eventually organ damage.

This is usually where most people develop the symptoms that give them a diagnosis of an autoimmune disease.

In some people, there can be a high level of autoimmune activity at play for some time before the tissue actually becomes damaged. You don’t want to keep waiting for the tissue to become damaged before you respond.
This is why it does not matter whether you notice any symptoms or not, if you have increased level of antibodies you need to take preventive action. 

By responding as early as possible, you can indeed prevent a lot of the damage downstream.

Neglecting or suppressing symptoms is not at all effective

The good news here is that it is not true that autoimmune diseases can only be managed or suppressed. 

The “gift” of having symptoms offers you an opportunity to take notice and start addressing the underlying problem. At the same time, medications can help to arrest or reduce the progressive and inflammatory damage to the body.

Recurring and seemingly symptoms like headaches, diarrhea, constipation, joint pain, lack of energy, and bloating may all be signs that something is out of balance. If you are ready and willing to make lifestyle changes, then over time you can reverse this disease dynamics of immune dysregulation.

You can read about how Dr Amy Myers reversed her condition with the help of Functional Medicine here.

However, to what extent you will be able to restore your tissue function is going to depend on that particular disease dynamic and the level of damage that has already taken place. 

I have written more about why you should not wait for an “exact” diagnosis here.

Your gut is the immune central

As I have mentioned earlier, about 70-80% of the immune system is your gut wall lining. The number of microbes as well as diversity plays a critical role, especially in the early stages of our life. 

It helps in informing and balancing and educating your immune system so that the immune system learns to be appropriately reactive- neither under-reactive nor over-reactive. 

Also, the collection of microbes (viruses, bacteria, yeast, amoeba, worms) in your gut acts as the modulator or controller of your immune system.

We know now that insufficient exposure to microbes when we are young through play outdoors, contact with animals, and being around pets, contribute to healthy immune function. These are all things that directly contribute to educating our immune systems so that we are less likely to struggle with diseases of hypervigilance in our immune systems.

A lack of such interaction also partly explains the exponential rise in childhood diseases such as allergies, asthma, eczema, and of course autoimmune diseases.  

10 most common causes of gut dysbiosis

Gut dysbiosis occurs when the microbiome is poorly cared for or fed and could be temporary, for example in response to the foods that we are consuming.

It could also be pathogenic or disease promoting due to dramatic changes in the diversity of the microbiome species.

Dysbiosis can be an overgrowth of something that is present in the human body that is usually in small amounts. Examples are overgrowth of a bacteria called H Pylori or an overgrowth of the yeast Candida Albicans. This yeast does not always promote disease itself but can do so under certain circumstances.

So the imbalance is not so much about the microbe itself but rather the effect it has on us. It’s more about the relationship that we have with the microbes in our gut and the effect that it has on our immune function.

And finally, there are many different contributors to dysbiosis ranging from powerful antibiotics to your food choices. 

Below is a list of 10 of the most common causes of gut dysbiosis in the modern world.

(I will be discussing these in more detail in my future live training and blog posts)

  1. Antibiotics
  2. Stress
  3. Acid suppressing medications
  4. Sucralose
  5. Poor digestion
  6. Chronic constipation
  7. Ongoing medications (NSAIDs, immunosuppressants)
  8. Toxins
  9. Steroid medications
  10. Lack of exposure to the natural environment

As the author and wellness activist Kriss Carr said

Quite literally, your gut is the epicenter of your mental and physical health. If you want better immunity, efficient digestion, improved clarity and balance, focus on rebuilding your gut health.


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Health Coach, author, blogger, podcaster, mom of two and avid reader

Before you get any further....
Hi, I'm Anindita!

I am a Functional Medicine certified Health Coach and AFMC practitioner. I help women with autoimmune conditions reverse their symptoms with their body as their guide

I work with women who want to go beyond symptom management, reconnect with their bodies and learn how to get well and stay well by tuning into their body's wisdom 

Learn more


“Autoimmune healing toolkit for women”

This toolkit will be focusing on the different kinds of tools you can use to create a healing environment like mindfulness, self compassion, journaling, stress management by reconnecting to your body's wisdom.
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