The Autoimmune Recovery Guide: Myths, Root Causes and Immune Balance

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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Autoimmune disease starts with dis-ease in our immune system.

Having one autoimmune condition makes you three times more likely to develop another.

This initially shows up in many different ways as irritations or minor symptoms such as headaches, indigestion, skin rashes, bloating, lack of energy, and fatigue. As the disease progresses, the symptoms become progressively worse and more intense. Our immune system produces more and more antibodies which may or may not result in any major symptoms in the beginning

Most people get a diagnosis usually only after there is already damage at both a cellular and tissue level.

The thing is, we need to identify the drivers and the root causes of the dysregulated immune
function so that we can prevent this from taking place. Otherwise the dysregulated immune system usually goes on to claim additional victims in the future. Leading to multiple autoimmune disease diagnoses in the future.

We can take measures and prevent ourselves from developing a second, a third, a fourth, and follow-on autoimmune disease diagnoses.

This is why no matter the diagnosis, we need to address the root causes and bring the immune system back into balance.

Once we stop suppressing our immune system and remove all the obstacles that prevent it from doing its job, it gets the message that all is right with the world.

It is once again able to do its job properly once more to protect us when necessary.

sad woman hug her knee and cry. Sad woman sitting alone in a empty room.

No chronic disease develops overnight and there is a certain disease progression that takes place over time. It starts with some amount of dis-ease in the body leading to symptoms that we can no longer ignore and finally a disease diagnosis.


Common misconceptions about autoimmune conditions

Before I get into the details about autoimmune conditions, I would like to bring awareness to a few prevalent myths about autoimmune conditions.

And sadly, these myths hold many people back from addressing the root causes of their chronic disease condition. 


1. The body is weak and vulnerable and develops disease out of the blue

This is the first and the most prevalent myth around autoimmune conditions that I have found in my coaching practice.

We are constantly bombarded with messages from different places which are completely wrong. This leads us to think that our bodies are weak and vulnerable. It also leads us to believe that we develop chronic diseases literally out of the blue, maybe even overnight. As a result, our disease diagnosis takes us completely by surprise. 

We don’t realise that our bodies have been dealing with some kind of imbalance or dysregulation for a long time. Initially minor symptoms show up which we often end up ignoring. It is only much later when there is enough tissue and finally organ damage that we get a disease diagnosis.

2. The immune system is confused and starts attacking the body’s own tissues for no reason whatsoever

This is the second myth that I want to bust today.

We often believe that our immune system starts running havoc, becomes confused and attacks our tissues. This is simply not true!

Very often, the reason why our immune system becomes hypervigilant and mistakes our own body tissue as foreign or as a threat has its roots in molecular mimicry.

For example, it mistakes gliadin, (a protein found in gluten for that in the thyroid gland in the case of autoimmune thyroid diseases like Hashimotos and Graves diseases) and the presence of a toxin or a microbe in a tissue for a long period of time as a threat.

Our immune system reacts strongly to this threat as well as the tissue it is a part of leading to tissue damage. This eventually leads to organ dysfunction and eventually organ damage. Nutrient poor foods, toxin exposure, and chronic stress all contribute to this kind of immune dysregulation and hypervigilance. 

I have written more about this below.

3. Immunosuppressive drugs are evil and they are the only solution for those with autoimmune conditions because they counteract and reverse the disease

Both of these statements could not be further from the truth. This is again one of the 4 powerful myths around autoimmune conditions that prevail.

Immunosuppressive medications are absolutely life saving and are necessary for preventing further damage to the tissue. This means that this medication helps us deal with the inflammation while we address the root of the autoimmune condition.

However, suppressing the immune system is not the same as dealing with immune dysregulation. Suppressing it does not help to heal from it by addressing the root causes. These medications often have dramatic downstream consequences including secondary autoimmune diseases or life threatening infections.

4. Autoimmune diseases are all somehow separate and unique and need to be treated completely differently

There are more than 80 autoimmune diseases that have been identified. However, all these autoimmune conditions are NOT really unique or separate

An autoimmune condition has at its root a certain level of immune dysregulation. And a chronically alert immune system leads to widespread inflammation that needs to be addressed.

This is irrespective of WHICH autoimmune disease you have been diagnosed with!

The “perfect storm” behind your autoimmune condition

In the case of autoimmune diseases, in particular, there is a specific loss of tolerance to self.

The immune system is unable to distinguish its own tissues and a real threat like microbes and toxins. It does have a number of inbuilt mechanisms that helps it to differentiate between host and foreign tissue. However, a hyper vigilant and long activated immune system that is reacting to threats continuously can become dysregulated over time.

A combination of factors referred to as the “perfect storm” is behind chronic autoimmune activation.

These are-

1.Enhanced intestinal permeability aka leaky gut

2. Genetic factors

3. A weak or imbalanced immune system

and a trigger.

Sometimes the trigger is a specific ongoing infection, a specific food or a highly stressful or traumatic phase in life. Underneath, there is a weak and imbalanced immune system that allows this chronic autoimmune activation. 

In this sense, autoimmune diseases are actually a dis-ease of the immune system.

As you see now, there are only a few root causes for chronic autoimmune activation.

There are more than 80 autoimmune diseases that fall into the same category. While they may have completely different names, these diseases are not really all that different since their underlying mechanisms are not all that different.

However, the names of autoimmune conditions don’t tell us anything about which organ or part of the body is being affected. And this confuses us further.

So while Graves and Hashimotos affect the thyroid gland, Lupus is a systemic disease, Multiple Sclerosis affects the brain and spinal cord and Psoriasis affects the skin.

Interestingly enough, autoimmune diseases affect women disproportionately more than men.

But there is one more thing, your gut plays a critical role in autoimmunity, and infact, in all chronic diseases.

“All disease begins in the gut”

– Hippcrates

The connection between gut health and immune function

More than 70% of your entire immune system resides in your gut.

This is called the “gut associated lymphatic tissue” or GALT.

In addition, your gut is also host to trillions of microbes of several hundred species. This is collectively called the “gut microbiome”. These microbes play an important role in maintaining optimal health through various mechanisms.

More importantly, it acts as a controller of how the immune system in your gut operates.

In order to ensure that nutrients pass through and can be transported to the rest of our body, our gut lining is semi permeable.

And any damage to this internal lining can lead to a cascade of health issues.

The cells that line the gut wall keep bacteria, undigested or partially digested food and toxins from entering our blood stream. This selectively permeable gut lining only allows digested food particles to enter the body under normal circumstances.

Both our immune system and our gut microbes protect this one cell thick gut lining.

Vector illustration set of intestinal bacteria (good bacteria, bad bacteria, opportunistic bacteria)

Above all, we feed and nourish our microbiome and they keep us healthy in various ways such as

  • breaking down complex carbohydrates
  • producing short chain fatty acids which are necessary for regulating immune function, maintaining integrity of our gut lining, healing
  • producing vitamins and nutrients like vitamin K, B12 and others
  • protecting against pathogens
  • training our immune system to differentiate between friend and foe
  • supporting detoxification

As you can see now, your microbiome has a profound effect on your overall health!

What is enhanced intestinal permeability (aka leaky gut)?

As mentioned earlier, enhanced intestinal permeability (aka leaky gut) is one of the three main factors comprising the perfect storm behind the autoimmune disease.

A healthy intestinal lining serves as an important protective barrier inside our body responsible for absorbing necessary nutrients while filtering out harmful substances.

However, when the lining of the gut barrier is compromised, it allows undigested food particles such as food proteins, toxins, and microbes, to enter into our bloodstream.

This usually triggers an immune system response because they identify these particles as foreign invaders and a threat. This immune response creates inflammation as a natural defense mechanism. However, chronic ongoing inflammation further damages the intestinal lining creating a vicious cycle of disease.

Causes of Leaky Gut

Some factors that can contribute to a leaky gut include:

  1. Unhealthy Diet: A diet rich in highly processed foods, sugars, gluten, dairy, and refined carbohydrates. This can create imbalances in gut bacteria and trigger inflammation.
  2. Chronic Stress: Sustained stress negatively impacts gut health by impairing nutrient absorption and altering gut microbiome balance.
  3. Infections: Gut infections such as bacterial overgrowth or candida can damage the intestinal lining.
  4. Medication Use: Certain medications like non-steroidal anti-inflammatory drugs (NSAIDs) and antibiotics. This can disrupt the delicate balance of gut bacteria, leading to increased intestinal permeability.
  5. Environmental Toxins: Exposure to toxins in food, water, personal care products, and the environment. This can harm the gut lining and compromise its integrity.

As mentioned earlier a hypervigilant immune system can become dysregulated over time and lose tolerance towards “self”

This is why addressing “enhanced intestinal permeability” (aka leaky gut) is key to reversing autoimmune disease.

Your protective immune system and immune dysregulation

Our immune system is designed to be really strong and keep us safe from any threats, internal and external.

This has helped our species survive over millions of years of evolution. But when we lose control over our pro-inflammatory and inflammatory responses, it leads to runaway and rampant chronic inflammation.

In the case of autoimmune diseases, the immune system has become imbalanced and overreactive causing a lot of inflammation. However, the immune system is neither broken nor dumb.

It is simply trying its best to adapt to the environment you are asking it to live in. In other words, chronic autoimmune activation is a form of “maladaptation” by your immune system (and your body) to ensure survival in the current circumstances.

However, if the immune system is hyper vigilant and activated for large periods of time, it may become unable to regulate itself and turn off this immune response.

In the case of autoimmunity, there is a skewing towards a proinflammatory response.

One of the main reasons for this is anti inflammatory mediators become proinflammatory mediators as a form of dysregulation.

In contrast, a healthy immune system is one that can self regulate and have an appropriate and balanced immune response. So it’s not really about how to boost your immune system.

And food, toxins and stress are three main factors that contribute to immune dysregulation.


-Low nutrient foods or processed foods filled with artificial colours/flavours and preservatives which are toxic and seem like a threat

-Nutrient poor foods lead to a weak immune system. It also hampers detoxification by reducing the availability of nutrients to an immune system that is already activated and alarmed

-Malabsorption impairs our body’s ability to get the nutrients it needs to activate a healthy immune response to any kind of threat


-Toxins use up a lot of our nutrients. This is because our body has to metabolise these and take them out of our system

-Ingredients in processed foods can look very much like toxins. It can be a physiological stressor as our immune system perceives them to be threats

-Toxins hamper our energy production by damaging our mitochondria (the powerhouse in our cells). It can also impact the ability of our tissues to work properly.


-Stress (chronic) impairs our ability to digest and absorb our foods leading to poor nutrient absorption.

-It also uses up more of those nutrients trying to break down the stress hormones themselves.

In the case of autoimmune diseases, all three challenge our immune system. This ultimately leads to an inappropriate and overreactive immune response.

This can also lead to a situation where our immune system tries to counteract too many things at the same time and become under reactive to another threat like a viral infection.

In other words, it is like an overworked police force that is stretched out too thin and unable to do its job properly.

Source: The School of Applied Functional Medicine

I have created a comprehensive guide “Autoimmune disease 101” which is a collection of books, podcasts, websites and other resources. You can sign up to receive it by clicking here.

Why you should NOT wait for an exact diagnosis

In complex chronic health conditions like autoimmune disease, it can often take years and in some cases even decades to get an “exact” and the most “accurate” diagnosis. 

Meanwhile, people keep waiting to get a proper and accurate diagnosis so that they can start on medications. In the meantime, this disease usually keeps on progressing and they keep getting sicker and sicker.

Chronic disease progression is not caused by any one factor and if the root causes and the triggers are not identified and dealt with then disease progression continues to take place unchecked.
In autoimmune conditions, a person can go on to develop several autoimmune diseases over time due to the very nature of this disease

It is of course important to get a disease diagnosis. This is so that they can start getting the treatment to stop the disease progression and prevent further damage.

The good thing is that the diagnosis and the treatment give them a chance to manage their symptoms. It allows them to improve their quality of life and gives them some time to make long term changes.

However, most people believe that this is where their responsibility ends. Or possibly this is all that medicine has to offer them. That the best they can do is to manage their symptoms.

Medications have their limitations

In conventional medicine, drugs are used to block, inhibit or alter the pathway of a particular biochemical reaction in our body which works extremely well in acute conditions. Treatment is organ-specific and works brilliantly in the case of emergencies and infectious diseases.

But this model is sadly insufficient and inadequate when dealing with chronic illnesses.

Because immunosuppression means slowing down the immune system so powerfully, it increases the risk of developing cancer or other life threatening infections.

The thing is…

laying the foundations of good health doesn’t depend on your disease diagnosis

you can always start where you are, with what you know about your health issues right now

you can always get better at a physical, emotional or spiritual level because healing is an “inside” job and does not depend solely on external resources

“Autoimmunity is our immune system’s attempt to adapt to all the new environmental agents and shifts that we’re being bombarded with every day. It’s an unsuccessful adaptation, but it is our body’s way of trying to fight back.”

-Dr Noel Rose

The spectrum of autoimmunity and the appearance of symptoms

The spectrum of autoimmunity is a progressive state of disease that runs from vibrant health at one end to degenerative disease at the other.

In between, you have a broad range of varied but related stages of disease that are connected to each other. In other words, at any point, either you are moving toward disease or you are moving toward health.

And we can suffer damage to our tissues long before any symptoms develop. 

When there is a slight elevation of antibodies, some people may experience some symptoms, while others with very high levels of antibodies may show no symptoms at all. Yet both these types of people are on the autoimmune spectrum.

And if they do not address the underlying factors, they will continue to progress along the spectrum until they are diagnosed with a chronic or deadly disease. 

You can read more about it in this excellent article here.

If the underlying factors continue to trigger your immune system, the immune system will respond more aggressively, causing inflammation. Ongoing and excessive inflammation leads to cellular damage. Continued cellular damage leads to tissue damage, which eventually leads to organ inflammation. Continued organ inflammation increases the severity of your symptoms, as you develop elevated antibodies to that particular organ. 

Finally, continued elevated antibodies to an organ lead to organ damage. This is the stage where you have enough symptoms to be diagnosed with an autoimmune disease.

But it doesn’t have to be this way!

Your body is constantly sending you messages in the form of symptoms, long before you can get a proper disease diagnosis.

Your symptoms are a “gift”

Symptoms occur when the body is not able to deal with the tissue damage being caused by the immune system.

However, our bodies give us enough early signs to let us know that something is wrong and needs our attention.

These are in the form of common but not normal symptoms like headache, anxiety, insomnia, depression, constipation, bloating, fatigue.

Source: The School of Applied Functional Medicine

Unfortunately, we often accept these symptoms as “normal” and we tend to ignore them.

You should neither accept these symptoms as “normal”, nor neglect and try to suppress them with medications.

These symptoms are your immune system’s and your body’s way of sending you a message. It is letting you know that there is an underlying imbalance or mechanism which needs to be addressed.

There is nothing wrong with taking medications for managing severe symptoms occasionally.

However, when you experience minor irritations or symptoms then take it as an opportunity to take action. This “gift” of having even minor symptoms is that it will force you to take notice and do something to address a problem. 

It is your window of opportunity to do something about these often seemingly unconnected symptoms before there is further disease progression and tissue damage.

And this is where your power lies, in bringing your immune system back into balance.

And if you want to get started today with this, then check out this free ebook “Autoimmune healing toolkit for women” . This is a guide focused on helping you work with your body’s wisdom to create a loving, healing environment and support your body’s healing process.

Bringing the immune system back into balance

Having a healthy and balanced immune response is necessary to heal from autoimmune disease.

It should be able to differentiate between a real threat and the body’s own tissues and develop tolerance to “self”.

A step by step approach to improving your gut health is where you need to start.

In Functional Medicine, we use a 5R approach to healing the gut and bringing the immune system back into balance. This is the starting point for healing from any chronic disease including autoimmune diseases.

  1. Remove first (e.g. stress, junk foods, constipation, harmful microbes, food allergen/sensitivities)
  2. Replace (e.g. digestive enzymes, stomach acid, adrenal support, bile acids)
  3. Reinoculate (e.g. probiotics, prebiotics, cultured foods, dietary fibre)
  4. Repair (e.g. L glutamine, aloe vera to repair the gut lining)
  5. Rebalance (e.g. stress relief, sleep and restorative practices, dietary changes, mindset)

In the case of autoimmune disease, eliminating inflammatory foods like gluten, dairy, soy, corn and eggs is where we usually begin.

Food remains the most important piece in the puzzle and the first step towards improving our gut health.

By eliminating these trigger foods which are causing your symptoms by creating chronic inflammation in your body you can begin working on healing your gut. The best way to discover your food sensitivities is to complete an elimination diet where you take out the most common inflammatory foods for a period of at least 6 weeks (preferably 3 months) and then add back the foods  to your diet one at a time to see if you have a reaction.

For this reason, an elimination diet remains a cornerstone in my practice of guiding my clients toward better health.

“Healing requires from us to stop struggling, but to enjoy life more and endure it less.”

~Darina Stoyanova

Laying a strong foundation by creating an environment for healing environment

Laying a strong foundation first when it comes to creating long term health is absolutely essential if we are to not only get well but stay well. 

However, many practitioners remain focused on improving certain lab markers and reducing symptoms at the expense of other foundational aspects of long term health creation.

If we do this without really helping the person understand and prepare for the journey ahead, the results are usually temporary.

You see, by not preparing ourselves mentally and emotionally to continue with the changes, we will revert back to our old habits sooner or later. Many people are so focused on their diet, supplements, medications, and treatments that they completely miss out on these important aspects of long term health creation.

Having a strong foundation when creating good health is KEY to sustaining the improvements over long periods of time

What do I mean when I say a strong foundation?

Things like

  • Eating hygiene and mindful eating practices
  • Sleep hygiene
  • Learning to read ingredients and nutrition levels for packaged foods
  • Knowing which foods to substitute and why
  • Nourishment beyond food like savouring rituals
  • Increasing body awareness and learning how to tap into the body’s wisdom for guidance
  • Self compassion and dealing with the inner critic

Without these strategies, most people find that their results are short lived.

lady in beach silhouette during daytime photography

Start where you are

Addressing the root causes of autoimmune disease is a highly effective way to restore balance and reverse autoimmune disease.

This means focusing on healing and repairing the gut lining, improving nutrient absorption, reducing inflammation, balancing the immune system, and managing stress. It is also important to be mindful of any potential food sensitivities or triggers as well as toxins in your environment.

By taking these steps to address the root causes of your disease, you can manage your symptoms more effectively and even prevent further damage.

Start by focusing on the areas that you need to prioritise.

And if you are not sure what these are, then start here.

  1. Your relationship with food and your diet
  2. Your stress response and your thoughts and behaviour
  3. Your daily choices

You can learn more about this by watching this video.

In my experience of dealing with women with chronic illnesses, I have found that these are common areas areas of concern that they need to prioritise right from the beginning.

By learning how to prioritise key areas of your life you can take steps today to lay a strong foundation and take care of your body taking into account the current circumstances in your life.

As William James had said

Act as if what you do makes a difference. It does.”

Anindita is India’s first Functional Medicine certified Health Coach from the Functional Medicine Coaching Academy (FMCA). She is also an AFMC Certified Practitioner from the School of Applied Functional Medicine.

She helps women with autoimmune conditions discover their own power to HEAL using her “BODY-WISE HEALING framework” with their bodies as their GUIDE so that they feel happy and healthy and at peace in their bodies

She is also the coauthor of a children’s book called “I have eczema so what?” based on the real life story of her daughter’s and family’s experiences

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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.
Sign up for the WAITLIST to receive the ebook when it is published!

Click HERE to sign up!


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