Now that we’ve sorted out macros and what foods you can digest we need to address micronutrients. This is what people typically think of when they hear the word “nutrition”. Unfortunately, when you listen to experts and don’t do any testing or food tracking you’re shooting in the dark without IR or a scope at a target that’s 300 yards out. So, testing and tracking are crucial for identifying your personal deficiencies. In lieu of that, I can share what population level research shows and what I personally see in my clients’s and my own diet.

TLDR:

Remember this maxim: Eat animals for micronutrients, protein and fat. Eat plants for carbs, fiber and polyphenols, especially their fruit.
Micronutrients, what most think of as nutrition, refers to vitamins and minerals
Vitamins are categorized as water-soluble or fat-soluble
Minerals are categorized as macro-minerals or trace-minerals
The simplest way to determine deficiencies is to track your food in Cronometer for a few days to see what’s missing. Some blood labs as well as Hair Tissue Mineral Anaylsis (HTMA) can give you clearer picture
The most micronutrient dense foods are beef liver and organs, egg yolks, raw dairy, oysters and fruit.

The first major concept to grasp is that animal products should provide the bulk of your micronutrients, protein and fats and plants should provide you fiber, polyphenols and carbohydrates. I covered the reasons for animal sourcing your protein and fats over the last two weeks here and here. However, what most people don’t know is that animal products have far more vitamin and mineral density than plants.

Plants have defense chemicals aimed at preventing predators from obtaining the vitamins and minerals they contain. These are called anti-nutrients. Phytates bind to minerals like calcium, iron, zinc, magnesium, and copper, making them less available for absorption. Oxalates can bind to calcium and other minerals, reducing their bioavailability. Glucosinolates present in cruciferous vegetables interfere with iodine uptake and thyroid function. Tannins and proteases inhibit plant protein digestion.

Most plants, with the exception of fruit and some fruit vegetables (vegetables with seeds) should be cooked to deplete these anti-nutrients. Please stop with the raw kale and spinach salad or you could very well end up with kidney stones - I personally know of two cases.

Another point of note is that plants want to primarily defend their offspring, their seeds. So they concentrate their defenses there. Grains, seeds, legumes, beans, and nuts are all seeds. They also contain the highest amount of PUFA.

Just because the nutritional facts on plants say it has 5mg of calcium or magnesium doesn’t mean you’re absorbing it due to these anti-nutrients.

Water Soluble Vitamins

Animal muscle and organ meat, bone broth, tallow, eggs and dairy are high density micronutrients sources. If you’ve crafted your bioenergetic diet with these, it will be chalk full of almost all of your micronutrients needs. However there are some exceptions that I’ve found.

The water-soluble vitamins are the all the B vitamins and vitamin C. The most common water-soluble vitamin deficiency I see is Vitamin B1. The highest bioavailable food source is nutritional yeast and ruminant liver with the recommended daily allowance (RDA) at 1.2 mg. However you’d have to eat copious amounts of these foods to meet your RDA. B1 is crucial for energy production being the rate-limiting cofactor for pyruvate dehydrogenase (PDH). PDH is the last step in converting glucose in glycolysis responsible for catalyzing the conversion of pyruvate to acetyl-CoA. It links glycolysis to the citric acid cycle in mitochondria. Additionally, B1 is also critical for a properly functioning vagus nerve (due to its role in energy production).

Dr Derrick Lonsdale showed in his research widespread B1 deficiency in modernized food systems and its relationship to dysautonomia aka vagus nerve dysfunction. I have personally seen clients heal from SIBO, idiopathic gut dysfunction, and improve glucose control with supplementing B1. Thiamax is what I use.

Side note, avoid ‘fortified’ or ‘enriched’ grains due to the use of folic acid (synthetic B9) and iron.

Folic acid consumption by poor methylators can cause mood and behavioral issues due to their inability to metabolize it effectively. This is particularly relevant for individuals with mutations in the methylenetetrahydrofolate reductase (MTHFR) gene, which is crucial for folate metabolism. Poor methylators consuming folic acid will often end up with major imbalances in dopamine and serotonin (read depression, anxiety, ADHD, OCD). If you are a poor methylator, like myself, its important to eat enough liver or supplement with methyl-folate. Keep in mind that if you are methylating sufficiently supplementing with methyl-folate and other methyle donors can cause problems. Know your status before supplementing.

Iron fortification often leads to iron overload which is highly oxidative. More on this in another article but for now enjoy this video demonstrating that iron added to cereal grains are actually iron filings.

Fat Soluble Vitamins

The fat soluble vitamins are A, D, E, and K and I often see deficiencies in all of these.

Both D and K2 are highly involved in proper uptake and distribution of calcium into bone and teeth. High dose K2 is frequently used to move calcium out of soft tissue and back into bone (ie in the case of high coronary artery calcium (CAC) scoring). Beef liver, egg yolks, hard cheeses like parmesan, and butter are good food sources of K2.

D should be generated from sun-skin interactions and be kept above 50 ng/mL for optimal calcium metabolism. Levels below this trigger parathyroid hormone (PTH). More on that here. If you’re unable to make enough D to be over 50, consider supplementing and make sure it also has K2 with it and its paired with magnesium.

Beef liver is the best source of retinol, the active form vitamin A and is easy to meet the RDA target with 5 ounces/week. Retinol is a major cofactor used in the StAR enzyme stimulating conversion of cholesterol into sex steroid hormones, critical for loading copper into ceruloplasmin resolving anemia, necessary for the production of sIGA, your first line immune defense in mucus membranes. Retinol also sensitizes your body to vitamin D thereby requiring less D.

Vitamin E is critical for a mitigating PUFA lipid peroxidation and it also lowers estradiol by inhibiting aromatase. The lipid peroxidation mitigation is precisely why its highest in nutsand seeds (the highest PUFA foods). Everyone has some amount of lipid peroxidation from high PUFA intake, whether current or historical. The recommended dose by Georgi Dinkov, bioenergetic expert, is 1.5mg for every 1 gram of PUFA consumed in your diet.

For its powerful benefits of mitigating PUFA and estrogen dominance, it’s an important long term supplement while PUFA depleting. I prefer Health Natura vitamin E.

Macrominerals

Minerals are much trickier to manage than vitamins. Fungi and bacteria in the soil are the key transporters of earth minerals to plants. With this biomass die-off due to industrial farming practices (tilling, pesticides, etc), the plants are more and more deficient. This means the overall micronutrient content of the food supply is much lower.

Morley Robbins, author of Cu:re your Fatigue, told me that the owner of an organic ranch tested the copper content of their beef liver and found it to be 3x lower than the reported USDA values. After a couple of years of remediating the soil with regenerative practices, it increased to the expected value. That being said, some minerals are quite abundant regardless.

One of the most important macromineral balances lies between calcium and phosphorus. In my article on calcium, I showed how a low Ca:P ratio creates metabolic havoc. The ideal ratio is 1.5:1. Keep an eye on these two in Cronometer to make sure. Most people are under-consuming calcium due to direct avoidance or lack of dairy. A low Ca:P ratio can significantly raise parathyroid hormone causing bone and tooth loss as well as a high arterial calcium. Phosphorus is high in muscle and organ meats as well as beans and legumes. It must be balanced with calcium to prevent these adverse effects. If you can tolerate dairy, its your best source of calcium. If not consider supplemental coral calcium.

Almost everyone is deficient in magnesium. Magnesium is vital for the biological activity of ATP (adenosine triphosphate), the primary energy currency of cells. ATP must bind to a magnesium ion to form Mg-ATP, which is the form used by over 300 enzymes. It is involved in multiple processes affecting muscle function, including oxygen uptake and energy production. For muscle cramps and hypertension this electrolyte is key. Chronically elevated cortisol significantly depletes magnesium too. Since it is very difficult to get enough from food, I recommend everyone take it as a supplement in some form. My favorite is topical magnesium chloride spray and epsom salt baths (magnesium sulfate). Both are highly bioavailable and excellent for acute muscle cramping too. In capsule format, magnesium glycinate is good. The RDA is 420 mg.

Lastly, very few people are getting enough Potassium (K), another important electrolyte. The RDA is 3400 mg. The balance between intracellular potassium and extracellular sodium is critical for maintaining cellular homeostasis and proper functioning of the electron transport chain in mitochondria.

Potassium is also intregral to muscle contraction, especially the vascular system. In conjunction with magnesium, lack of potassium leads to muscle cramping and hypertension. Both can easily be managed with sufficient fruit, potatoes, squash and avocado.

Trace Minerals

Among the trace minerals I find imbalances and deficiencies in Copper and Zinc.

Copper is a central mineral in complex 4 of the electron transport chain and is responsible to its ability to absorb near infrared and red light. Copper is also the core mineral in ceruloplasmin, the protein responsible for regulating iron metabolism, hemoglobin, and thus oxygen transport in the blood. Almost all iron-deficient anemias are misdiagnosed and are actually copper-deficient anemias.

Zinc deficiency increases aromatase activity (conversion of T to Estradiol), decreases 5α-reductase activity (the conversion of T into the most potent androgen DHT), and impairs the conversion of the thyroid hormone T4 to the active form T3 lowering metabolic rate.

Oysters are the highest food source of zinc and beef liver is the highest source of copper. They are antagonistic so taking them away from one another is important, especially if supplementing. Zinc gluconate and copper bisglycinate are the preferred capsule forms. The RDA for zinc is 11 mg and copper is 1 mg.

Aside from polyphenols in fruit which act as prebiotics for your microbiome, choline is probably the most important non-vitamin, non-mineral micronutrient. Choline is a precursor for acetylcholine, an important neurotransmitter that regulates muscle contraction, supports memory and cognition and controls autonomic nervous system functions.

Phosphatidylcholine (PC) is downstream of choline in the CDP-choline pathway. Choline and PC are essential for liver function and preventing fatty liver disease by aiding in fat metabolism and transport of lipids from the liver. PC is a key component of bile, assisting in fat digestion. Choline helps lower homocysteine levels, reducing cardiovascular disease risk.

With regard to energy production, PC regulates lipid composition within mitochondrial membranes. This is crucial for maintaining proper mitochondrial bioenergetics.

Cardiolipin (CL) is a unique phospholipid found predominantly in the inner mitochondrial membrane, where it constitutes 10–15% of total mitochondrial phospholipids. It stabilizes the structure and function of ETC complexes. CL interacts directly with proteins like complex IV, facilitating electron transfer between complex III and complex IV. PC directly supports cardiolipin in this function.

The best food source is egg yolks with a general adequate intake (AI) recommendation of 500mg/day - equivalent to 3 yolks/day. Commercial eggs, regardless of their organic status, are very high in PUFA. So if you’re working on PUFA depletion, or require quick and stable remodeling of mitochondria lipid membranes, I recommend Mitolipin. Its a fully saturated PC product.

To recap, the most common micronutrient deficiencies I see are:

Vitamin B1
Vitamin A
Vitamin D
Vitamin K2
Vitamin E
Calcium
Magnesium
Potassium
Copper
Zinc
Choline

Testing and tracking food are the ideal ways to know your personal deficiencies. Do your best to obtain micronutrients from food and if you can’t, supplement. Always look for supplements that are additive free.

To your health,

Jonathan

This is for informational purposes only and should not replace professional medical advice. Consult with your physician or other health care professional if you have any concerns or questions about your health.

Most Common Micronutrient Deficiencies