These 6 Key Nutrient Deficiencies Are Linked to Autoimmunity: What You Need to Know

This article was originally published by our friend Dr. Amy Myers

Your immune system is a complex machine, and just like a car, it can’t function properly without the right fuel. There are six key nutrients that I consider to be the premium fuel for your immune system. If we are deficient in any or all of these key nutrients we are at risk for our immune system to go haywire attacking the body’s own tissues and leading to autoimmunity.

That’s why when an autoimmune patient comes to me for help, I not only check for things such as infections, toxins, and stress, which might be sabotaging their immune system, I also check for key nutrients it might be lacking. Restoring optimal levels of these nutrients is an important step in reversing autoimmune disease, and also preventing another autoimmune condition from developing.

6 Key Nutrient Deficiencies Linked to Autoimmunity

Here are the six nutrients that research has linked to autoimmune disease, and that I most commonly see in my autoimmune patients.

1. Vitamin D

Even if you live in a warm climate and get plenty of sunlight, your vitamin D levels could be below optimal. This is particularly problematic for autoimmune patients because vitamin D plays a critical role in the immune system. It regulates and prevents autoimmunity by stimulating regulatory T cells, which are responsible for differentiating between dangerous invaders and “self” cells. When vitamin D promotes these cells, it teaches the immune system to not attack itself.

Vitamin D also supports your ability to fight off viral and bacterial infections that can trigger or worsen autoimmune conditions.

2. Omega 3s

Because our modern day diet tend to contain more polyunsaturated vegetable oils instead of quality animal fats, many Americans are deficient in Omega 3 fatty acids. Studies have shown that omega 3 oils enhance B cell activation and select antibody production, which can lower the inflammatory response and help your immune system fight off pathogens.

3. B vitamins

B vitamins do more than just provide energy for our cells. They also control immune function, hormones, mood, sleep, nerves, circulation, and digestion. Vitamin B12, for example, supports the production of white blood cells, which are essential components of the immune system. When you are low in B12, your white blood cell count is lowered, which weakens your immune system and makes it more susceptible to mistakenly attacking your own cells.

4. Selenium

Selenium may be a little-known mineral, but studies show that it is essential for regulating excessive immune responses and chronic inflammation in autoimmune diseases. It is also a vital nutrient for proper thyroid function, and studies show that increasing selenium in autoimmune thyroid patients decreases their thyroid antibodies. I talk more about this in my upcoming book, The Thyroid Connection.

5. Zinc

Zinc affects multiple aspects of the immune system, from the skin barrier to gene regulation within lymphocytes (a type of white blood cell). In fact, zinc is essential for the production of white blood cells and studies show that people with zinc deficiency are more susceptible to pathogens.

6. Magnesium

Magnesium, which is important not only for immune function but also heart health, is a mineral most people are chronically low in due to high levels of stress and high-sugar diets (sugar depletes magnesium levels). Magnesium deficiency has been shown to cause an increased production of proinflammatory cytokines, which raise your overall level of inflammation, contributing to autoimmunity.

What Causes Nutrient Deficiencies in Autoimmune Patients?

Now that we know which nutrients play a critical role in the immune system, let’s look at why autoimmune patients are often low in them.

A Nutrient-Poor and Inflammatory Diet

This one is pretty obvious, but if you aren’t eating these nutrients, your body won’t have enough of them. If you haven’t started following any of The Myers Way® protocols, you’re likely eating lots of white flour products, refined sugars, and processed foods. While these foods may taste good, they are completely devoid of nutrients, and what little vitamins they offer typically have to be added synthetically.

In addition to nutrient-poor, processed foods, a diet high in inflammatory foods can also cause nutrient deficiencies. These inflammatory foods, including gluten, grains, legumes, nuts and seeds, nightshades, eggs, dairy, sugar, and caffeine, not only stimulate your immune system, they also cause leaky gut.

A Leaky Gut

We know from Dr. Alessio Fasano’s research that virtually all autoimmune patients have a leaky gut. What you may not know is that when your gut is leaky, the junctions in the intestinal walls that keep your GI lining tight become “loose” allowing food proteins, bacteria, yeast, and viruses to enter the bloodstream. Additionally, some people have blunted villi — the small hair-like projections that absorb nutrients — which means they can’t absorb foods properly and become deficient in vitamins and minerals, even if they’re getting plenty of them in their diet. This causes a wave of inflammation that triggers or worsens autoimmunity.

Gene Mutations

Common gene mutations such as MTHFR significantly reduce your ability to convert certain nutrients that contribute to methylation, including B vitamins, choline, folate, and more. VDR mutations can cause low vitamin D, and mutations that control Sulfation, a liver detoxification pathway, can cause zinc deficiency. If you have one or more of these gene mutations, then you might be getting plenty of nutrients from your diet or supplements, but your body simply isn’t able to optimally utilize them.

How To Test For Nutrient Deficiencies

If you have an autoimmune disease and want to get your levels tested, here are the labs that I recommend.

Standard Lab Tests

There are standard lab tests your doctor can order to assess your nutrient statuses. However, conventional medicine relies on “normal” reference ranges that are far from optimal. I talk about the lab ranges I prefer to use in my books, The Autoimmune Solution and The Thyroid Connection.

Comprehensive Nutrition Panel

If you are working with a Functional Medicine doctor, I highly recommend getting an ION® (Individual Optimal Nutrition) Panel. The panel analyzes both urine and blood samples to measure levels of key vitamins, minerals, antioxidants, and organic, fatty, and amino acids. It provides a very complete picture of a patient’s nutrient status and offers very insightful clues to what might be causing their health conditions.

How to Prevent or Overcome Nutrient Deficiencies

Restoring optimal levels of these key nutrients can be done! By upping your dietary intake, and addressing the underlying causes of your deficiencies, you can replenish your levels and strengthen your immune system. Here’s what to remember.

Eat a Nutrient-Dense Diet

Getting your nutrients through food is always the ideal route, so you’ll want to add plenty of these foods to your diet:

  • Vitamin D- fatty fish, grass-fed or pasture-raised proteins, and organ meats
  • Selenium- garlic, turkey, liver, and red meat
  • Magnesium- dark leafy greens like spinach and chard, figs, fish, avocado, and bananas
  • Zinc- oysters and seafoods, grass-fed beef and lamb
  • Omega 3- grass-fed meats, fatty fish, flax and chia oil
  • B vitamins- leafy greens, animal proteins, fresh and dried fruits, seafood, avocados

Heal Your Gut

Healing your gut is one of the most important steps to take in your autoimmune journey. It will not only improve your ability to absorb nutrients, it will dramatically reduce your inflammation and calm your immune system.

I use Functional Medicine’s 4R Approach to healing the gut:

  • Remove the Bad – Get rid of gut infections and toxic and inflammatory foods
  • Restore the Good – Add back the essential ingredients for proper digestion
  • Reinoculate with Healthy Bacteria – Re-establish a healthy gut flora
  • Repair the Gut – Rebuild the mucosal lining of your gut

You can learn more about the 4R Approach in this post, and in my book, The Autoimmune Solution.

Learn About Your Unique Genetic Needs

If you’re curious about your genes and how they can cause nutrient deficiencies, you can order a genetic test through They send you a kit to collect a saliva DNA sample, and then they provide you with basic genetic information and all of your raw data. You can then enter your raw data into one of several third-party tools to translate it into a report that shows you which genetic mutations you have, and what that means for your health. Livewello is one option, as is Genetic Genie. From there, I recommend working with your Functional Medicine doctor or Wellness Coach to figure out the right diet and supplements for you.

Add In High-Quality Supplements

Although optimizing your diet, healing your gut, and eating for your genetics go a long way, you may need to add in supplements as well. The unfortunate truth is that our nutrient-depleted soil, high-stress lifestyles, and toxic environments make it very difficult to get all of our nutrients from food alone. Fortunately, high-quality supplements can step in to fill the gap.

Here are the supplements I recommend for everyone with autoimmunity take on a daily basis:

  • Multivitamin – A daily multivitamin to build a foundation of optimal health. The one I carry in my store contains the full recommended levels of selenium, magnesium, and zinc.
  • Vitamin D – When supplementing with vitamin D, be sure to choose one that combines D3 (the active form of vitamin D) with vitamin K2 because these nutrients are complementary and work together for proper immune, brain, hormone, and bone health. The K2 also prevents calcium buildup in your heart from the use of vitamin D.
  • Omega 3 – Often, Omega 3 supplements come from fatty fish which can also be high in mercury. When supplementing make sure that the Omega 3 supplement you choose is from a reputable source that verifies through a 3rd party that they have no detectable mercury in their product.
  • B vitamins – The best source for this is my Vitamin B Complex which contains all eight B vitamins in a form that is easily absorbable. If you are have one or two MTHFR mutations, please use my Methylation Support that includes premethylated B vitamins and other important nutrients needed for for methylation.


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