Doctor Doni

5 Steps to Reverse Autoimmunity and Autoimmune Diseases

Dr. Doni Wilson explains what autoimmunity is, the many health issues it can cause, and how to recover naturally, even when your doctor says there is no cure.

Autoimmunity, ALS, Crohns disease, Graves disease, Rheumatoid arthritis, Celiac disease, Alzheimers, Epstein Barr virus, Hashimotos diseaseMany of my patients come to me after having been diagnosed with autoimmune conditions such as Hashimoto’s disease, Celiac disease, or rheumatoid arthritis.

Others may suffer from a range of troublesome health issues that have not yet been diagnosed but indicate a possible connection to autoimmunity.

Still others may have a family history of neurodegenerative disease, Alzheimer’s, or fibromyalgia – all of which may be linked to autoimmunity – and are looking for ways to prevent these conditions from arising in themselves.

Autoimmunity lies at the root of so many serious health conditions. Yet, it is so misunderstood by the public, and (in my opinion) not often treated effectively by mainstream medicine.

For these reasons, I am writing this article today, in which I will answer some of the most frequently asked questions about this important health issue:

What Is Autoimmunity?

Your immune system is designed to attack “foreign invaders” that enter your body, such as unhealthy bacteria, viruses, toxic substances, and allergens. In some cases, however, your immune system can become confused and start destroying cells of one or more of your body’s tissue or organs, mistaking them for foreign cells.

We call this malfunction “autoimmunity,” meaning your body is essentially attacking itself (“auto”). Left unaddressed, autoimmunity can cause many debilitating – and sometimes life-threatening – conditions.

What Causes Autoimmunity?

For the longest time, scientists did not understand what causes autoimmunity. In fact, they are still studying autoimmunity and discovering more each year. Many researchers have concluded that STRESS – in any of its various forms – is the original trigger for autoimmunity.

“Stress” isn’t just emotional or psychological, but also physical, including damage from environmental toxins, toxins (called LPS) caused by overgrowing bacteria in the intestines, viral infections (such as Epstein Barr virus), and even stress caused by certain foods (such as gluten).

If stress were the only factor triggering autoimmunity, we’d probably all have some form of autoimmune condition. But genetics also play a role. Your genes determine whether your immune system is predisposed towards developing autoimmunity or not.

This is what I refer to as your Stress Fingerprint. Your genetics plus your stress exposure.

Being predisposed doesn’t mean you will automatically develop autoimmunity; but if you are exposed to one or more of these stresses, it can “wake up” and trigger your genetic tendency.

When that happens, a cascade of stressed/confused immune and nervous system signals spread through the body, eventually creating antibodies intended to protect us from our own selves, which leads to inflammation, pain, and tissue damage.

What Conditions Can Autoimmunity Cause?

Over 100 serious health conditions are autoimmune in origin. And more are being added to the list each year as research reveals autoantibodies involved in the pathogenesis. Each condition affects you differently, depending on which part(s) of your body your immune system is attacking. Some of the most common autoimmune conditions are:

Additionally, recent studies show these conditions are at least in part related to autoimmunity:

What Symptoms Could Be Signs of an Autoimmune Issue?

While each of the conditions listed above has its own specific symptoms, there are other, more general, symptoms that could indicate an underlying autoimmune issue:

How Do Most Mainstream Medical Professionals Address Autoimmunity?

Unfortunately, many mainstream practitioners are slow to recognize or diagnose autoimmunity issues. Some will tell you that nothing is wrong, or that your symptoms are simply signs of aging that you need to accept passively.

Even once you have been diagnosed with an autoimmune condition (which is often only after the symptoms have progressed extensively), most practitioners will treat you by prescribing medication to decrease inflammation, suppress your immune system, and/or manage some of your symptoms or pain.

At first impression, suppressing the immune system makes sense, and is necessary in some cases. However, immunosuppressive and anti-inflammatory medications, such as prednisone, suppress both the autoantibodies and your healthy immune system, leaving you more vulnerable to other health concerns, such as bone loss, diabetes, heart disease, and cancer.6

Can Autoimmunity Be Reversed?

Most mainstream medical practitioners consider autoimmunity to be an irreversible condition, and will tell you that once it turns on, it cannot be turned off. But I believe this notion is perpetuated because these practitioners are not asking the fundamental question:

“How can we address the original CAUSE, so we can STOP the body’s signal to create autoimmunity?”

That is exactly the question I ask when I work with a patient with autoimmunity; and by asking that question, I have seen autoimmunity vanish. Decades of experience have taught me that if we can get rid of the trigger(s) that switched ON the autoimmune response, we stand a good chance of switching it OFF.

Knowing that the trigger for autoimmunity is stress, then it follows that the solution is to address the stress and help your body to recover from stress. This is the strategy I use in the Stress Remedy approach (read more about it here) for various conditions including autoimmunity.

So, my answer to the question, “Can autoimmunity be reversed?” is, in most cases:


Dr. Doni’s 5 Steps to Reverse Autoimmunity

There is no one-size-fits-all description of autoimmunity; it will look different for everyone. That is why, whenever patients come to me with any kind of autoimmune issue, the first thing I want to find out is what is going on in ALL their bodily systems, so we can identify the root cause(s) of their condition.

I also want to get a comprehensive picture of their stress/toxin exposure and see how this is impacting those systems.

Finally, I want to analyze their genetic health profile, to see if there are indications of a predisposition towards autoimmunity (I have met very few practitioners, even in the field of naturopathy, who include this as part of their approach).

To find out this information, I use various specialty health panels to check for adrenal distress, leaky gut, dysbiosis, oxidative stress, and methylation problems.

Once we understand what triggered their autoimmunity in the first place, we can design a step-by-step plan to re-optimize and rebalance their bodily systems, which gradually decreases the severity of the autoimmunity until it is no longer an issue.

While there are many stress patterns that can trigger autoimmunity, the five most common I have seen in my patients are:

  1. Adrenal distress (maladaptive stress syndrome)
  2. Leaky gut (intestinal permeability)
  3. Imbalanced microbiome (dysbiosis)
  4. Oxidative stress
  5. Impaired methylation8

All these things can be discovered through carefully selected health panels. With the information we obtain from these reports, I help my patients make diet and lifestyle changes, address imbalances, and eliminate environmental triggers.

Essentially, I help support their bodies so autoimmunity can switch off, and they can get back to living a healthier, drug-free and symptom-free life.

Here’s an overview of how I typically work through these five influencers of autoimmunity.

STEP 1: Address adrenal distress

The adrenal glands make several hormones, including cortisol and adrenaline. We need these to be at optimal levels based on the time of day (higher in the morning than at night) because they communicate with major systems in our body including the immune system, digestion, nervous system, and all the other hormones in the body.

Adrenal distress happens when we are exposed to ongoing daily stresses (which we all are) that shift the amount and timing of the cortisol and adrenaline produced. That shift sends a signal of stress to the immune system, sometimes triggering autoimmunity.

Adrenal distress also increases the likelihood of viruses, such as Epstein Barr Virus (associated with autoimmunity), becoming active, leaky gut worsening, and bacteria in the intestines becoming disrupted. This, in turn, causes methylation to become impaired, and can increase overall oxidative stress on the body, making it even harder to cope with the stress.

We can measure both cortisol and adrenaline levels so we know exactly how stress has affected your body. Once we get the cortisol and adrenaline back on track (using nutrients, herbs, and de-stressing activities), the immune system will also start to come back into balance.

STEP 2: Identity and address leaky gut

When our digestive system is healthy, it only allow water, glucose, amino acids, digested fat molecules, and nutrients to get through to the other systems of the body.

Exposure to environmental stresses – including toxins, pesticides, medications, infections, gluten, caffeine, alcohol, and even injuries – can increase the damage to the intestinal cells.

When the cells lining the walls of the small intestine become damaged, we can develop “intestinal permeability” – also known as leaky gut.

When this happens, the junctions between cells become enlarged, allowing undigested food and bacterial toxins to “leak” from within the intestines, through the intestinal lining, to the space underlying.

Our immune system sits in this space on the other side of the intestinal wall, like a guard at the door. When the “wrong” stuff comes through, the guard notices and sends signals of distress throughout the body. These distress signals can trigger autoimmunity, as the immune system starts protecting us not just from the foreign invader, but from nearby or similar-looking tissue (even though it is part of our own body).

We can identify leaky gut by doing a specialized IgA and IgG antibody food sensitivity panel. Not just any panel, but a panel that will provide accurate and clear results showing which foods are triggering an immune response. Once we have that information, we will know which foods for you to avoid and the severity of leaky gut. Find the panel I recommend here.

To reverse leaky gut, we need to:

Once leaky gut has been healed, the autoimmune response will also stop, because the immune system is no longer getting triggered.

STEP 3: Rebalance your gut microbiome

The relationship we have with the trillions of bacteria living inside our bodies is one of the most significant determinants of our health. The bacteria living in our intestines (microbiome) are important not only because they make nutrients (like vitamin K), but also because they also communicate with our immune and nervous systems.

Our gut bacteria eat what we eat; different foods will feed different bacteria. The quantity of certain bacteria will also increase or decrease when we take certain medications or we are exposed to certain stresses.

Virtually everything we do influences the bacteria living inside of us, from the amount of time we sleep, to the number of times we fly on an airplane, to how much sugar or gluten we eat. Even your mindset can affect which bacteria will thrive and which will struggle to survive.

Many people take probiotics or fermented foods (such as sauerkraut and kombucha) believing they will increase the good bacteria in their microbiome. But I have found these strategies on their own are usually inadequate to address gut imbalances (and could cause imbalances).

Moreover, what many people misunderstand is that it is possible to have too many good bacteria, or too many of certain types of bacteria. I think of it like a garden. Too much of a particular plant can create just as many problems as too many weeds.

You want to have the right amount of the right kinds of bacteria in the gut.

We can find out which bacteria are growing in your intestines by doing a specialized stool panel, called PCR, which measure bacteria based on their DNA. This new technology allows us to determine whether you have a good balance of bacteria, or an overgrowth of bacteria.

Autoimmunity of various types has been associated with the overgrowth of certain bacteria (called dysbiosis). These overgrowing bacteria can “leak” through the leaky intestinal lining we discussed earlier, and/or produce toxins (called LPS) that can leak through. Either of these “leaks” can trigger autoimmunity as the immune system tries to protect you from them.

Practitioners and patients have tried everything to address bacterial imbalances, from antibiotics (to kill abnormal or overgrowing bacteria) to fecal transplants (to put in more good bacteria). But there are many natural – and longer-lasting – ways to bring balance back to the gut microbiome.

What I have found works best is to focus on a long-term strategy that includes:

Be prepared for the healing process to take some time; but be assured as well that re-optimizing the balance of bacteria in your gut will also remove the signals that may have triggered your autoimmune response.

STEP 4: Reduce oxidative stress

“Oxidative stress” is like rust, but inside our cells instead of on metal. It is what causes aging, decreased energy, decreased memory, wrinkles, and just not feeling well.

If a doctor ever says, “You’re just getting old,” what (s)he means is that you have the signs of oxidative stress.

We can’t avoid oxidative stress altogether – and we wouldn’t want to. It’s a normal process in our cells that helps us fight off infections and recover from injuries. Our bodies also naturally make anti-oxidants to counter oxidative stress. We are also exposed to both oxidative stress and anti-oxidants through our food, air, and environment.

The problem occurs when our bodies are exposed to too much oxidative stress without enough anti-oxidants to counter-balance it. That’s when oxidative stress starts damaging cells and triggering autoimmunity.7

We can measure oxidative stress in urine panels that identify something called 8OHdG. We can also look for levels of lipid peroxides and glutathione to tell us whether oxidative stress needs to be addressed.

To reverse autoimmunity, we need to counteract oxidative stress and help the body regain optimal production of antioxidants such as coQ10 and glutathione.

This is a complex topic, which I explain more in this article: Why Your Body Needs (and Wants) Stress.

STEP 5: Optimize methylation

Methylation is the process by which our bodies turn B-vitamins into the substances that create energy for our bodies, protect our cells, maintain our mood and mental clarity, help the liver to process toxins and estrogens, and protect our DNA.

While those of us with MTHFR and other methylation-related gene SNPs have an increased risk of methylation issues, anyone (even people without those SNPs) can experience decreased methylation at some point in life.

Exposure to environmental toxins (such as cigarette smoke, glyphosate, parabens, and phthalates) and heavy metals (such as lead and mercury) can impair the body’s methylation process. Stress, inflammation, oxidative stress, toxins from imbalanced bacteria in the gut, and nutrient deficiency (due to leaky gut, for example) can all contribute to methylation problems.

When methylation is impaired, genes that increase one’s tendency toward autoimmunity can get “switched on,” making it more likely that an autoimmune condition begins.

We can measure methylation starting with a blood test called homocysteine. And if we need to get more detailed, we can measure S-adenosylmethionine and more.

With the information we have now about how to re-optimize methylation and turn genes back “off” again, it is possible to stop autoimmunity.

Restoring healthy methylation can be more complex than simply taking methylfolate. In fact, I find it is essential to follow a 5-step process to prepare your body before adding folate. Read more about my approach to MTHFR here.

If you recently found out that you have an MTHFR mutation and you’d like to learn more about what that means and what is involved in my approach to optimizing methylation, you may choose to take my MTHFR group class on your own right now because we have a recorded version available here.


If you have been struggling with autoimmunity, I truly hope this article has shown you that your condition is NOT a life sentence, as some other health professionals may have told you.

I passionately believe that our bodies have the ability to heal when given the right support.

I believe this because I’ve seen it happen – both in myself and in my patients. Healing from autoimmunity does require diligence, diet, and lifestyle changes. You may find the process profoundly cathartic, leading you to examine your entire approach to living and make changes you never thought you could make.

If you’re thinking you’d like to “dip your toes in the water” before committing to a long-term health plan, you might want to start by reading my book, The Stress Remedy, or by doing one of my Stress Remedy Programs (there is a 7-day and a 21-day version).

Or, if you want some instant self-help, you could start for free by signing up to Weekly Wellness Wisdom newsletter, where you will receive my 35-page eBook, A Guide to Adrenal Recovery, as my special gift.

Finally, if you are serious about getting healthy again and would like my personal support, I invite you to learn more about my Autoimmunity and Toxicity Solutions Consultation Package. Whether you currently have autoimmunity, or you have a genetic predisposition to autoimmunity or a health issue that could develop into autoimmunity, this comprehensive health overhaul will help guide you back to health.

Whatever you decide, be assured that your body is perceptive, and it will notice and pick up on ANY positive changes you make. So, start small – but start SOMEWHERE. And observe for yourself what is possible.

Until next time, I wish you well.

–Dr. Doni
20th March 2018

*Please keep in mind that any and all supplements—nutrients, herbs, enzymes, or other—should be used with caution. My recommendation is that you seek the care of a naturopathic doctor (with a doctorate degree from a federally-accredited program) and that you have a primary care physician or practitioner whom you can contact to help you with individual dosing and protocols. If you ever experience negative symptoms after taking a product, stop taking it immediately and contact your doctor right away.


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