Your immune system is a complex machine, and like a car, it cannot function properly without the proper fuel. There are six key nutrients that are the premium fuel for your immune system. If we suffer from key nutrient deficiencies, we run the risk of our immune system running rampant and attacking the body’s own tissues, leading to autoimmunity.

When an autoimmune patient comes for medical help, not only do I check for infections, toxins, and stress that could be sabotaging your immune system, but I also look for key nutrients that might be missing. Restoring optimal levels of these nutrients is an important step in reversing autoimmune diseases and also in preventing the development of other autoimmune diseases.

6 nutrient deficiencies linked to autoimmunity

These are the six nutrients that research has linked to autoimmune disease, and that are most noticeable in autoimmune patients.

Vitamin D

Even if you live in a warm climate and get lots of sunlight, your vitamin D levels may still be suboptimal. This is particularly problematic for autoimmune patients because vitamin D plays a critical role in the immune system. 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 not to attack itself.

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

Omega 3

Because our modern diet tends to contain more polyunsaturated vegetable oils rather than quality animal fats, many Americans are deficient in Omega 3 fatty acids. Studies have shown that omegas 3 oils enhance the activation of B cells and select the production of antibodies, which can reduce the inflammatory response and help your immune system fight pathogens.

B vitamins

B vitamins don’t just provide our cells with energy. 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’re low in B12, your white blood cell count drops, weakening your immune system and making it more susceptible to mistakenly attacking your own cells.


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 increased selenium in autoimmune thyroid patients lowers their thyroid antibodies.


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.



Magnesium, which is important not only for immune function but also for heart health, is a mineral that most people are chronically low due to high levels of stress and diets high in sugar (the sugar reduces magnesium levels). Magnesium deficiency has been shown to cause increased production of pro-inflammatory cytokines, increasing your overall level of inflammation and 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 see why autoimmune patients are often low in them.

A nutrient-poor and inflammatory diet

This one is pretty obvious, but if you are not eating these nutrients, your body will not have enough of them. You probably eat a lot of white flour products, refined sugars, and processed foods. While these foods may taste good, they are completely lacking in nutrients, and the few vitamins they offer generally 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, which include gluten, grains, legumes, nuts and seeds, nightshades, eggs, dairy, sugar, and caffeine, not only boost the immune system, but also cause a leaky gut.

Leaky gut

We know from the research that virtually all autoimmune patients have a leaky gut. What you may not know is that when your gut is perforated, the junctions in the gut walls that keep your gut in alignment “loosen” allowing proteins, bacteria, yeast, and viruses to enter the bloodstream. Also, some people have amputated villi, tiny capillary projections that absorb nutrients, which means that they cannot absorb food properly and are lacking in vitamins and minerals, even if they consume a lot in their diet. This causes a wave of inflammation that triggers or worsens autoimmunity.

Genetic mutations

Common genetic mutations like MTHFR significantly reduce your ability to convert certain nutrients that contribute to methylation, including B vitamins, choline, folic acid, and more. VDR mutations can cause low amounts of vitamin D, and mutations that control sulfation, a liver detoxification pathway, can cause zinc deficiency. If you have one or more of these genetic mutations, you can get many nutrients from your diet or supplements, but your body simply cannot use them optimally.

How to test for nutrient deficiencies?

If you have an autoimmune disease and get tested to see how your nutrient levels are. He orders them to analyze through urine and blood samples to measure the levels of vitamins, minerals, antioxidants and essential fatty acids and amino acids. They provide a very complete picture of a patient’s nutritional status and offer very insightful clues as to what could be causing your health conditions.

How to prevent or overcome nutrient deficiencies?

The good news is that you can restore optimal levels of these key nutrients. By increasing your dietary intake and addressing the underlying causes of your deficiencies, you can replenish your levels and strengthen your immune system. This is what you must remember.

Eat a diet rich in nutrients

Getting your nutrients through food is always the best option, so you’ll want to add many of the following foods to your diet:

  • Vitamin D: fatty fish, protein from grass-fed meats including organ meats.
  • Selenium: garlic, turkey, liver and red meat.
  • Magnesium: dark leafy vegetables like spinach and chard, figs, fish, avocado, and bananas.
  • Zinc: grass-fed oysters and shellfish, beef and lamb.
  • Omega 3: grass-fed meats, fatty fish, flax oil, and chia.
  • B vitamins: green leafy vegetables, animal proteins, fresh and dried fruits, seafood, avocados.

Heal your gut

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

  1. Eliminate the Bad: Eliminate intestinal infections and toxic and inflammatory foods.
  2. Restoring the Good – Re-adding the essential ingredients for proper digestion.
  3. Introduce healthy bacteria – restores a healthy intestinal flora.
  4. Repair the gut – rebuild the lining of the lining of your gut.

Add high-quality supplements

Although optimizing your diet, healing your gut, and feeding your genetics are important, you may also need to add supplements. 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.

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