Autoimmune Disease: A Functional Medicine Guide To Symptoms, Causes + Natural Treatments

Autoimmunity occurs when the immune system mistakenly over-reacts to the body’s own tissues, attempting to destroy them with inflammatory cells. The immune system is, of course, meant to protect against viruses, bacteria, and other intruders, so why would it suddenly mistake the body for an enemy?

Actually, in most cases there is nothing sudden about it. Many people are experiencing low-grade autoimmune reactivity years before they have suffered enough tissue damage to warrant a formal diagnosis through the conventional healthcare system. And it’s a major problem.

Research from the medical journal Nature estimates that about 25 percent of us have some sort of dysfunction of the immune system, and according to the American Autoimmune-Related Diseases Association, 50 million Americans have a diagnosable autoimmune disease. (1) Meanwhile, millions more have autoimmune spectrum problems with “no explanation” for their symptoms. 

Why Are Autoimmune Conditions On the Rise? 

Researchers aren’t sure yet what causes autoimmune disease, but the primary theories include a genetic susceptibility being triggered by an immune system response to toxins; food proteins like gluten and casein leaking into the bloodstream through a compromised gut lining; or chronic viral, bacterial, yeast, or parasite infections. 

All of these involve out-of-control inflammation, which is an immune system trigger. This inflammatory-immune response can both cause and increase intestinal permeability or leaky gut syndrome, further perpetuating the inflammatory-immune cycle. (2) 

Our increase in exposure to toxins, our stressful modern lifestyles, and the standard American diet filled with processed foods and refined carbohydrates are among the likely factors that have led to such a staggering increase in the prevalence of autoimmunity. 

Is Autoimmune Disease Caused By Genetics Or Lifestyle?

The old view of genetics was that it was an immutable force and that if your family had a certain health problem, it would be just a matter of time before you got the same disease, unless you were very lucky. 

Today, we know it isn’t that simple. The field of epigenetics explores and demonstrates how environmental factors influence DNA expression. Genetics can give you the tendency to develop an autoimmune disease, but it is your lifestyle choices and your environment that determine whether those particular genes get switched on or off. In other words, our exposures may largely determine our genetic expression and the strength or weakness of our immune system.

One Stanford study published in 2015 looked at genetic and lifestyle health factors in 210 healthy twins, both identical and fraternal. (3) What they found was remarkable: 58% of the immune system was almost completely determined by environmental and lifestyle factors, and 19% of the immune system was largely influenced by environmental and lifestyle factors.

This is great news because it means 77% of the immune system is influenced or determined by things we can control. 

The Influence Of Chemicals, Processed Foods, and Environmental Toxins

In the past 100 years, even in just the last few decades, there has been a disturbing increase in production of and exposure to chemicals, processed foods, and environmental toxins, and the fact is that our genes are struggling to keep up. 

Take the effect of fast food on your Th17 cells, for example. Their purpose is to fight pathogenic bacteria and fungi, but their overreaction has been linked to autoimmune disease. (4) Researchers found that a high-salt diet negatively affected Th17 cell reactions and increased autoimmune problems. Our fast food society is filled with salt levels far beyond what anyone would get eating a natural diet. This is just one of the many triggers that can cause an inflammatory autoimmune response in genetically susceptible individuals.

This is where functional medicine is a huge player. By looking at root cause triggers and using natural tools of diet and lifestyle, you can learn what your body needs to calm your over-reactive autoimmune responses.

Are You On the Autoimmune Spectrum?

The sad reality is that in the conventional medicine model, the immune system has to destroy a significant amount of tissue for an autoimmune condition to be officially diagnosed. 

For example, there has to be 90 percent destruction of the adrenal glands to be diagnosed with Addison’s disease, or severe destruction of the neurological and digestive systems to be diagnosed with multiple sclerosis (MS) and celiac disease, respectively.

In a conventional medical setting, a diagnosis won’t come until the end stages of autoimmune conditions when it may be too late to treat or reverse it. In my telehealth functional medicine practice, I believe in detecting and treating autoimmune disease and chronic inflammation before it does too much unnecessary damage. 

This is why I look at autoimmunity as a spectrum. You can be on the low end, with some reactivity, or in the middle, with significant symptoms that are still not conventionally diagnosable, or at the end stage, when symptoms are so intense that a doctor finally has a label for your condition. We need to focus on catching signs of autoimmune disease early, and preventing it from progressing. 

You can read more about the inflammation and autoimmune spectrum in my book, The Inflammation Spectrum.

Three main stages of the autoimmune spectrum:

1. Silent Autoimmunity: There are positive antibody labs but no noticeable symptoms. Your doctor will likely tell you that you are probably fine, or to come back next year and re-test.
2. Autoimmune Reactivity: There are positive antibody labs and symptoms, but still not enough to warrant a formal diagnosis.
3. Autoimmune Disease: There’s enough body destruction to be diagnosed.

Among my patients, I find that quite a few of them are at Stage 2. They clearly know something is off but don’t have significant enough markers for traditional medical providers to give a diagnosis. I believe everyone on this spectrum deserves to feel better as soon as possible, and they can. 

How To Spot Autoimmune Disease Early

Some early symptoms of autoimmune reactivity include achy muscles and joints and fatigue. I’ve also written in the past about how some cases of unexplained depression could be due to autoimmune reactivity of the brain. 

Early detection of an autoimmune disease before extensive damage, could give you a sort of grace period in which to address the issue, stop the progression, and in some cases reverse the autoimmune spectrum symptoms. Start the autoimmune disease prevention process with a complete set of functional medicine labs to detect early signs of autoimmunity. Some research suggests that antibodies can show up on labs several years before the diagnosis of many autoimmune diseases. (5) 

I like to run predictive autoimmunity labs, which allow us to detect abnormal immune responses against many parts of the body. Some of the more common antibodies we find are:

• Stomach: Parietal cell antigens, which are associated with gastric autoimmunity
• Thyroid: Thyroid peroxidase antigens, which are associated with Hashimoto’s disease
• Brain: Synapsin antigens, which are associated with inhibited neurotransmitter release
• Adrenals: 21 hydroxylase (adrenal cortex) antigens, which are associated with autoimmune endocrine disorders
• Gut: Tropomyosin antigens, which are associated with inflammatory bowel disease (including Crohn’s disease and ulcerative colitis)
• Joints: Arthritic peptide antigens, which are associated with rheumatoid arthritis.

This type of testing may be beneficial for someone who:

• Has unexplained symptoms but “normal” labs
• Has gluten intolerance
• Has leaky gut syndrome
• Has already been diagnosed with another autoimmune disease

To be clear, functional labs like this are not used to diagnose autoimmune diseases, which is still done in the mainstream medical setting. We use labs like this to investigate underlying factors and tailor a health program to improve these issues, based on the types of antibodies we find and other individual factors.

Can You Prevent Autoimmune Disease?

While there is no certain way to prevent autoimmunity, there are several ways you can support your body to lessen the likelihood or slow or stop the progression of an autoimmune condition. We will explore some triggers to avoid, as well as supplements, foods, and lifestyle tips you can implement to support healthy immune function. 

Let’s dive into some of the ways you can support your body whether you are aiming to prevent or reverse autoimmune disease symptoms. 

15 Surprising Triggers Of Autoimmune Conditions

I’ve already covered many of the likely contributors to the autoimmune explosion we are seeing. But zooming in more, what triggers or worsens autoimmune disease in daily life? Let’s take a look at some of the biggest triggers. 

#1. Eating a Modern Diet

Our food culture has changed drastically in a relatively short period of time with the development of human agriculture and the onslaught of manufactured food and food chemicals. Human genes haven’t yet had the chance to adapt to these extreme changes, and this mismatch between modern food and ancient human biochemistry has, according to many experts, significantly contributed to the rise of autoimmune disease.

For example, humans eat far more grains than they ever did pre-agriculturally, and we know there is a clear link between grains and autoimmune conditions. Getting the proper food intolerance testing done can be the first step for many to regain their health. Until you know what you personally are reactive to, you cannot know for sure what foods to avoid to cultivate health. I’ll focus next on some of the most common culprits I see. 

#2. Gluten

The infamous “G” word is a protein that’s found in wheat, barley, spelt, rye, and other grains, and is linked to an increased risk of autoimmunity. The most obvious example is the autoimmune condition celiac disease; however, the emerging condition non-celiac gluten sensitivity (NCGS) may also be connected to autoimmunity. (6)  

NCGS doesn’t necessarily show up clearly on a test like celiac does, but a simple gluten elimination diet can help you figure out how gluten is affecting you. If you think this may apply, try eliminating gluten for a good 90 days and pay attention to whether your symptoms get any better.

#3. Gluten-Free Grains

Many people with autoimmune problems already avoid gluten, but still consume non-gluten grain foods like corn, oats, and rice. As well-intentioned as that may be, these grains can be just as damaging as gluten for people who are sensitive to them (and this is common with people prone to autoimmune issues).

One reason is that the proteins in these grains are very similar to gluten, and an overactive immune system may mistake them for gluten anyway and begin an attack. Just as with gluten sensitivities, symptoms do not have to be gastrointestinal in nature. A flare-up of any autoimmune symptom can occur with exposure to grains. Running immunological blood tests or trying to go grain-free can help detect or rule out this trigger.

#4. Quinoa

A favorite in the health community, so-called pseudo-grains like quinoa are high in proteins called saponins, and these can be inflammatory and damaging to the gut lining, causing an immune response in the body. Soaking and rinsing quinoa can reduce the gut-damaging effect, but for many with serious autoimmune conditions this is not enough and avoiding quinoa altogether is a more effective strategy to quell this inflammation and symptom response.

#5. Sugar

It should be no surprise that sugar is on this list, but I’m not just talking about the stereotypical junk food. There are many popular “healthy” junk foods that are not good for autoimmune conditions, even if they are labeled as healthy, organic, or natural. 

Terms like “organic turbinado sugar” or “agave nectar” on a food label may sound less insidious than “white sugar,” but to the immune system, it’s all sugar. Try using fewer sweeteners and added sugars all around for better health.

#6. Dairy

Casein, the main protein found in cow’s milk and other dairy products, can be a trigger for runaway inflammation in the body for those who are susceptible. Ghee/clarified butter and plant-based “dairy” products like almond milk may be preferable and safer for some people. Some people with autoimmune disorders can also handle fermented dairy, like grass-fed whole yogurt or kefir. 

#7. Nightshades

Members of this plant group that consists of tomatoes, peppers, potatoes, eggplants, goji berries, and some spices (like cayenne pepper) contain certain alkaloids in their skins which can cause an inflammatory response in the bodies of some susceptible people. (7) 

#8. Instant Coffee

Beloved by many on a busy work day, instant coffee (not brewed coffee) may cause an inflammatory-immune response in some individuals with autoimmune disorders. Why is instant coffee worse? Likely due to the chemicals used in the manufacturing of instant coffee (and not the coffee itself). 

That said, certain individuals respond negatively to regular brewed coffee as well. I run food reactivity blood labs on my patients to see what underlying food triggers they may have, but you can also test yourself by phasing out coffee. After the caffeine headache clears, you may find you feel a lot better. Again, this isn’t everyone, but it’s one possible factor to consider. 

#9. Artificial Sweeteners

Artificial sweeteners like saccharine (Sweet’N Low), sucralose (Splenda), and aspartame (Equal and NutraSweet) are in many diet and zero-calorie drinks and foods, but even though people may believe that reducing calories with these products is good for health, these sweeteners can significantly harm the gut microbiome, triggering inflammation and autoimmunity. 

#10. Stress

Research has found chronic mental stress to be a trigger for autoimmune diseases, and accordingly, many of my patients noticed the onset of their autoimmune health problems during a rough time in their lives. (8) Stressful life events can be the tipping point for an autoimmune response. Stress management techniques like deep breathing and meditation can help to reverse the stress response.

#11. Toxins

Modern living has its benefits, but it has also created a planet so toxic that we’re constantly struggling to avoid exposure to pollution, food additives, heavy metals, cosmetics, and the toxic chemicals in everyday tasks like cleaning and personal hygiene. These toxins play a role in many different types of autoimmune disease including Hashimoto’s thyroiditis. (9)

#12. SIBO

Small intestinal bacterial overgrowth, or SIBO, occurs when normal bacteria of the microbiome expand beyond the large intestine into the small intestine, where they are not supposed to be. Chronic SIBO can lead to or exacerbate leaky gut, which can then trigger autoimmunity throughout the body. 

#13. Gut Dysbiosis

Your gut microbiome significantly influences not only your immune system, but your brain, hormones, and genetic expression. Gut dysbiosis (an imbalance between beneficial and pathogenic bacteria in the gut microbiome) is clearly linked to autoimmunity. (10)

You don’t necessarily have to be experiencing gastrointestinal symptoms to be affected by dysbiosis or pathogens in the gut. I run a specific two- or three-day stool lab to uncover these often undiagnosed factors in autoimmunity. Getting this kind of test can be informative regarding your microbiome balance.

#14. Leaky Gut Syndrome

Increased gut lining permeability, or a “leaky gut,” is a common precursor to autoimmunity. Since all of the above-mentioned triggers can lead to leaky gut syndrome, a leaky gut can be considered a casual trigger, as well as a symptom, of an autoimmune condition. Taking steps to repair the gut can therefore help to avoid triggering flares as well as help to reverse the autoimmune response.

#15. Infections

Infections, including bacterial, parasitic, fungal, and yeast infections, are associated with just about every autoimmune condition. This could be due to the fact that the majority of our immune system is found in the gut microbiome, so when infections enter the gut, they can alter immune activity.

This can become a trigger for autoimmune thyroid disorders (AITD) and other autoimmune conditions. For example, in one study, 36% of Graves’ disease patients had evidence of a recent viral or bacterial infection. (11) 

The Best Nutritional Supplements For Autoimmune Disease

As Hippocrates, the father of medicine, said, “Let food be thy medicine, and medicine thy food.” When there is a lack of nutrients in the foods you’re consuming, the genetic switch for autoimmunity could be triggered, but flooding your body with those nutrients can help reverse that trigger. 

#1. Vitamin A 

Vitamin A is essential for a strong immune system, and vitamin A deficiency has been linked to autoimmune diseases such as rheumatoid arthritis and type 1 diabetes. (12, 13) Researchers suspect the reason has to do with our dendritic cells, which send out a “red alert” at the sign of a supposed invader, to stimulate immunity. (14) This “calm down” message can be strongly supported by vitamin A, making it one of the best natural supplements for autoimmune disease.

True vitamin A, called retinol, is only found in animal products including fish, shellfish, fermented cod liver oil, and liver. Plant carotenes, a precursor to vitamin A, are found in sweet potatoes and carrots but the conversion rate to the usable retinol is very weak. In fact, research suggests that in healthy adults, just 3% of beta-carotene gets converted in a healthy adult. (15) 

#2. Vitamin D 

Known as the “sunshine vitamin,” this nutrient is essential for many metabolic and immunological pathways in the body, but specifically, vitamin D works in conjunction with vitamin A and has been shown to dampen the inflammatory response. With autoimmune conditions like inflammatory bowel disease, multiple sclerosis, psoriasis, systemic lupus erythematosus (SLE), and rheumatoid arthritis, Th17 cells run out of control, but Vitamin D can help quell that inappropriate response.

As with vitamin A, vitamin D is most abundant in animal and dairy fats, but the best way to get it outside of supplementation is by soaking up some time in the sun – about 20 to 60 minutes a day, depending on your complexion. Consider getting tested every few months to ensure your vitamin D levels are within a healthy range.

#3. Curcumin

Curcumin, the active ingredient found in turmeric, has very powerful anti-inflammatory properties and can be incredibly helpful for those with autoimmune conditions. (16) This is one of my go-to supplements for autoimmunity and basically all chronic diseases involving inflammation (in other words, basically all chronic diseases). It also comes with minimal to no side effects. 

#4. Probiotics 

Given the strong role that the gut microbiome and gastrointestinal health play in autoimmunity, supporting the gut with supplemental, beneficial bacteria (probiotics) can be very helpful. Studies have shown that probiotics can reduce inflammation and modulate immune function in autoimmune conditions. (17) Remember that the majority of the immune system lives in your gut! 

#5. Fish Oil

Omega-3 fatty acids, found in fish oil supplements, have been shown to improve immune system function. (18) Potential benefits for autoimmunity have been demonstrated in type 1 diabetes, Crohn’s disease, ulcerative colitis, multiple sclerosis, juvenile arthritis, and other conditions. (19)

10 Tools To Prevent and Reverse Autoimmune Inflammation

While it’s true that, at least when it comes to autoimmune conditions, once that genetic switch has been turned on, it doesn’t turn off again, there is still much you can do to dampen and reverse your autoimmune response. 

Better yet, this can be done in a way that dramatically reduces or even eliminates symptoms, all without prescription drugs or bouncing around from specialist to specialist with no clear answers. Beyond the supplements listed above, here are a few tools to help prevent further autoimmune disease and in some cases even reverse your symptoms.

#1. Have Your Gut Permeability Tested

Most of your immune system resides in your gut, but when its protective lining is compromised, an autoimmune response can be the result. To determine the integrity of the gut lining, I run labs so my patients and I can address this major underlying component to regaining health.

READ MORE: Types Of Gut Microbiome Testing + How It Works | Dr. Will Cole 

#2. Restore the Integrity of Your Gut Lining

Once you know more about the extent of your gut permeability and whether you have any secondary issues like small intestinal bacterial overgrowth (SIBO) or chronic bacterial, yeast, or parasitic infections, you can work in a more targeted way to heal your particular issue, ideally with a functional medicine practitioner. Here is some great general information on natural ways to heal the gut.

#3. Get Your Antibodies Tested

Depending on your specific autoimmune condition, you will likely have specific elevated antibodies, which are proteins that are a part of your immune defense system. Knowing your specific antibody levels will help you do two things: 1) Gauge your healing progress in a measurable way, and 2) Get clues to any associated autoimmune disorders you may have, as many people with autoimmunity have more than one area where this manifests. Catching any additional autoimmunity early is key for improving overall wellness. 

#4. Nix the Gluten

Not everyone necessarily reacts negatively to gluten, but if you have an autoimmune condition, you don’t need a lab test to tell you that gluten should be on your no list. This protein, which is found in wheat, spelt, rye, and barley, tends to be especially inflammatory and immune-provoking for those with many autoimmune conditions. (20)

Though I do run comprehensive gluten intolerance labs for some autoimmune cases to demonstrate definitively the level of intolerance, and to give my patients objective motivation for removing gluten, I can tell you from vast experience that gluten should be off the list for anyone with this health issue. If you aren’t yet convinced, just try eliminating it completely for 60 days, then reintroducing it. This can be a helpful test to demonstrate to people how strongly symptoms return when gluten is reintroduced.

#5. Consider Cross-Reactive Foods 

Sometimes, bodies with overactive immune systems can attack something just because it resembles something else. This is called molecular mimicry, and it can happen when the proteins in a food look like gluten. (21) Even gluten-free grains like corn and rice can flare up the immune system in some people – something I see frequently in my practice. Find out if you are having any cross-reactions with the foods you are eating by removing them for 60 days and reintroducing them one at a time to determine if your symptoms return or flare. This can be very helpful for people who have cleaned up their diet but are still having symptoms.

#6. Detox Regularly

People with autoimmune conditions tend to have altered detoxification pathways, so giving them a helping hand on a daily basis can help get the body back into shape. One of the easiest ways to do this is to eat a variety of green leafy vegetables like kale and spinach, and avoid sugar and processed foods that make the toxic load heavier. These two things alone can make a big difference in your health.

READ MORE: Exactly Why + How You Should Detox According To A Functional Medicine Expert | Dr. Will Cole 

#7. Add Powerful Food Medicines Into Your Diet

Foods such as green tea and turmeric have been shown to dampen the autoimmune response in the body, especially in the brain. (22) Have a cup of green tea and add turmeric to your food daily for a huge anti-inflammatory, antioxidant, and immune-balancing boost.

#8. Replace Refined Table Salt With Natural Sea Salt

Table salt is highly processed and has been shown to aggravate and increase some autoimmune conditions. (23) Go with more natural salt that contains trace minerals.

#9. De-Stress Daily

When it comes to the “fire” of autoimmunity, stress is the gasoline. In fact, stressful events are often the triggers for autoimmunity. Many of my patients say they noticed the onset of their condition during a particularly stressful life event. We can’t avoid stress completely (and we don’t want to), but regular practice of meditation, yoga, tai chi, or other stress-relieving practices can help you better manage stress and balance your immune system. Even a few minutes of breathwork at the end of a long day can be incredibly helpful. 

#10. Go For Glutathione

Many people with autoimmune conditions are deficient in this important nutrient, the body’s master antioxidant. (24) If you tolerate them, eat plenty of sulfur-rich vegetables like onions, cabbage, and broccoli to aid in methylation, a biochemical pathway that produces glutathione naturally.

Your Efforts Will Be Worth It

Autoimmune disease is not “curable” but you can take back your quality of life with natural interventions that might even put your autoimmune disease into remission. Consistently practicing the steps outlined here is a great way to begin reversing autoimmune disease symptoms and living a vibrant, healthy life. 

I’ve seen countless people with persistent autoimmune symptoms completely regain their health and well-being through natural lifestyle changes like these. If you’re looking for more personalized guidance, please book a consult with our telehealth functional medicine center.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe. 

Photo: Stocksy

Read Next: Dysautonomia: Types, Symptoms, Root Causes, And Treatment Options

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