Nutrient Deficiencies and Autoimmune Disorders

We all know that vitamins and minerals are necessary to function well, but oftentimes the clients I work with are deficient in several. When there’s a lack of nutrients in the body, the genetic “switch” for autoimmune may be triggered, which is why it’s so crucial to keep your levels optimal. There are five nutrients that I often find to be low with my autoimmune clients, and I’ll address those below in detail.

5 Crucial Nutrients You May Be Missing

Vitamin D

This is a big one for autoimmune, and honestly, just in general it is a top deficiency. And right now with COVID, it’s more important than ever to get this vitamin up because of its impact on the immune system. This is one of those nutrients that people often get wrong. For example, you run your labs, and discover your levels are low. You take a D2 supplement for a few months, retest and…levels are the same. Why?

To start, D3 is often more effective than D2 (read a study here). On top of that, many times practitioners will prescribe a high dose for a period of time. The problem with that is that D is a hormone. It must be titrated up slowly to maximize absorption. So the zero to 100 method isn’t the most effective, but instead, low and slow.

Complicating this further, vitamin D needs co-factors in order to convert it to it’s final “usable” form- magnesium and K2. So if your magnesium or vitamin K2 levels are insufficient, guess what? Your D won’t go up. Annoying, right? And, if you throw on top of that some gut issues or bile insufficiency (especially those with a missing gallbladder), then don’t expect those D levels to increase at all.

Key Takeaways:

Opt for D3 instead of D2 if you supplement, and take it with some fat since it’s a fat-soluble vitamin. Make sure your magnesium and K2 levels look good, or supplement with them while you’re supplementing with D3. If you know you’ve got some gut issues, or are missing a gallbladder, consider that you may have additional work to do to maximize absorption. Get outside and aim for 20 minutes of sun daily, without sunscreen or sunglasses. And check those levels annually, striving to keep your levels between 40-70 ng/nL.


Oh magnesium, one of my favorite minerals to talk about. It’s a running joke between me and some clients. Not sleeping well? Take magnesium. Leg cramps? Magnesium. Constipation an issue? Get some magnesium.

It’s not because I love to supplement, but it’s because more than 70% of the population is deficient in it. And, magnesium deficiency can lead to a whole host of issues: sleep, anxiety and depression, thyroid issues, blood pressure, and more (you can read all about it here).

Even with eating tons of dark leafy greens, pumpkin seeds, and dark chocolate, I encounter clients with magnesium deficiency (even with a squeaky clean gut). We have topsoil erosion and stress to thank for that.

Key Takeaways:

Check your RBC magnesium levels (I find them to be more accurate than serum magnesium) and make sure they’re in the upper 1/3 of the reference range. When opting for a supplement, I prefer magnesium glycinate, threonate, or malate. Citrate is great for stimulating the bowels if that’s an issue. Take your supplement with food for maximum absorption.


This little guy flies under the radar, and because of that I find a good chunk of my clients are deficient in it. This nutrient is a component of glutathione, which is the bodies master antioxidant. So by ensuring selenium is adequate, glutathione can also be improved. Low level increase your risk for an inflammatory issues as well as premature aging (no thanks). This is one that’s super easy to get via food- just one to two Brazil nuts daily will do the trick.

Key Takeaways:

If you opt for a supplement, 200 micrograms is where I’d cap out. Food-wise, just 1-2 Brazil nuts is all you need. Even though it’s a common deficiency, it’s also easy to overdo selenium, so make sure you’re not eating Brazil nuts by the handful.


This is another one of my favorite nutrients. Not only is it responsible for multiple aspects of the immune system, but also helps repair damaged DNA and is a major player in your central nervous system. It’s also a component in more than 200 enzymes in our body. Oh, and in times of sickness, zinc is also a top go-to for my family. So it’s kind of a biggie.

Zinc does work in tandem with copper, so it’s important to make sure you’re getting both (kind of like sodium and potassium). But, I often find that zinc is lower (especially in those with autoimmune disorders) due to the American diet.

Key Takeaways:

If you can eat oysters, great. They’re the best source. Otherwise pumpkin seeds are a good plant-based source. If you supplement, the body can’t really break down more than 30mg at a time, so no need to megadose. 15-30mg is likely all you need.

B vitamins

Ahhh…love me some B vitamins. This is my energy go-to. But, it’s so much more than just increasing energy. B vitamins are responsible for methylation, which is a fancy term for a biochemical process that happens every second in our body. But, some times that process is hindered. Perhaps it’s due to genetics, stress levels, or toxins.

When methylation becomes an issue, that’s when the immune system takes a hit, as well as neurotransmitters and cellular energy. We need this functioning properly. Besides the usual ‘eat the rainbow’ that I preach to my clients, B vitamins are also found in organ meats, eggs, and bee pollen.

Key Takeaways:

If you’ve never taken a B complex, start super slow with it as you don’t want to ‘overmethylate’ and create anxiety or other issues. Usually I advise less than 1/2 a capsule in the morning. Additionally, like the others above, there are a few variations in B vitamins. I typically suggest starting with a methyl complex if you’ve not taken them before, and avoid anything with folic acid. Another great way to get more B’s is to take an organ supplement. Personally I can’t stomach the texture and taste of organ meat, so I take a high quality supplement instead.

So final thoughts on this all- get your levels checked! I’m a big fan of the NutrEval to check nutrient status as it’s one of the most comprehensive tests on the market. Remember, if you’re dealing with deficiencies, that creates an imbalance in the body leaving you more prone to infections, new symptoms, and obviously an increased risk for autoimmune.

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