2 More Common Nutrient Deficiencies (and What to Do About Them)

In our rush to ditch processed, boxed, packaged, refined foods, we run the risk of missing out on several key nutrients that they come fortified with, courtesy of food producers (what would we do without them?!) who recognize that the people who live off their nutrient-free food products need some actual nutrition amidst the sugar and the crunch. In case you don’t know what I mean, swing through the cereal aisle of a grocery store sometime and check out the nutrition facts for a few products. A single serving of something like Frosted Flakes is fortified with most of the B-vitamins, vitamin D, vitamin C, vitamin A, iron, and folic acid, often the full RDI. Well, it turns out these nutrients are attainable through actual food. No, really. So instead of relying on Frosted Flakes for our iron, or Wheaties for our zinc we can eat real food. But sometimes the real foods that contain the nutrients we need aren’t the ones we think to eat, and this can become a problem.

That said, let’s look at a couple more nutrients (I covered five last week) that I suspect people may be missing out on.


Manganese. How many of you have scanned this word and assumed it was magnesium, perhaps misspelled? I know I have, but I also know that it’s one of those trace minerals that regulates dozens of enzymatic reactions in the body, and that it’s really important. It’s also a primary constituent of one of our favorite endogenous antioxidants, manganese superoxide dismutase, which is active in our mitochondria.

Deficiency Symptoms

  1. Asthma – Low manganese levels are consistently associated with childhood asthma, while one study found a similar relationship between dietary manganese intake and asthma in adults.
  2. Ineffective utilization of several key nutrients – Choline (see below), thiamin, ascorbic acid, and biotin all require adequate manganese to be utilized by the body.
  3. Low thyroxine (thyroid hormone T4) – Manganese is essential in the production of T4.
  4. Osteoporosis and joint pain Bone mineral density doesn’t just come down to calcium (or magnesium). Manganese also plays a small but important role in skeletal health. Consider the story of Bill Walton, basketball legend and the greatest hyperbolist in the history of Western Civilization, who was diagnosed with osteoporosis at the height of his career after a series of broken bones that would not heal. The cause? A macrobiotic diet that left his serum manganese levels entirely undetectable.
  5. Low HDL – In women fed a manganese-deficient diet, HDL plummeted (PDF).

Why Might Deficiency Occur?

  1. Insufficient intake of manganese-rich foods. This is an obvious one. If you don’t eat manganese, you’re not going to have enough of it. If you’re only eating beef, shy away from berries, hate shellfish, and avoid all nuts all the time because of omega-6, you may be missing some manganese.
  2. Iron overload. This isn’t a true “cause” of deficiency, but for those with hemachromatosis, or excessive iron absorption and retention, manganese can reduce the absorption of dietary iron. Primal eaters – who are almost invariably eating iron-rich meat on a regular basis – may be getting less manganese than they need, especially if they’re avoiding most of the richest sources of the mineral.

Where to Get It

  1. Nuts. In descending order from richest, hazelnuts, pine nuts, pecans, walnuts, mac nuts, and almonds are all good sources of manganese.
  2. Bivalves. Mussels are the best source, followed by oysters and clams.


Shoot for 2-5 mg per day or so.


Choline is the precursor for acetylcholine, a neurotransmitter involved with memory; it’s an integral component of two important phospholipids; and the liver uses it to process fats and package lipids. The real authority on choline is Chris Masterjohn of the Daily Lipid blog. In fact, I’ll refer to his series of choline posts from time to time, because they do a far better job of explaining than abstracts from PubMed.

Deficiency Symptoms

  1. Fatty liver – The research is pretty clear that a choline deficiency is majorly responsible for fatty liver.
  2. Lowered VLDL – Without choline, very low-density lipoprotein synthesis in the liver is disrupted. While reducing VLDL might make your lipid panel happy, it also sets you up for developing fatty liver, since the fat isn’t being packaged into lipoproteins for dispersal.
  3. Elevated ALT levels – Elevated alamine transaminase levels could indicate liver problems, which are often caused by a choline deficiency.
  4. Elevated homocysteine – A choline deficiency results in a reduced capacity to methylate homocysteine (PDF).
  5. Impaired memory – Since choline is the precursor for acetylcholine, a choline deficiency often manifests as a memory impairment. One study even found that choline supplementation improved memory in humans who were deficient.

Why Might Deficiency Occur?

  1. You’re still scared of dietary fat and cholesterol. The best sources of choline come packaged with fat and cholesterol. I imagine this fear explains the “silent epidemic” of fatty liver across America that Chris Masterjohn discusses, but don’t let it get to you.
  2. You’re still scared of offal. Yeah, yeah, it’s icky, it has a very distinct taste, your grandma used to overcook liver and force you to eat it, whatever. Liver and other offal bits are awesome and essential.
  3. You’re not scared of dietary fat and cholesterol. Huh? Doesn’t this contradict number one? Not exactly. Most of you are all about the fat, and that’s awesome, but eating more fat increases the need for choline. This doesn’t mean you have to reduce the fat; you simply have to increase your choline intake (luckily, Primal fat sources are also often choline sources, as you’ll see below).

Where to Get It

  1. Liver and egg yolks, and probably other sources of offal (brain, kidney, etc).
  2. If you aren’t eating liver and/or egg yolks, you’re going to be deficient in choline. Other sources, except for maybe beef cube steak, pale in comparison.
  3. Supplement. Cell membranes (as in eggs) contain phosphatidylcholine, so look for that version if you intend on supplementing (but getting it through food is so much more fun).


550 mg for men and 425 mg for women, bare minimum. Pregnant, soon-to-be-pregnant, and breastfeeding women should increase their intake considerably, as low choline intake is associated with neural tube defects. Ah, heck, I bet everyone could do with a little more choline in their diets, especially if you’re not scared of dietary fat.

Let me reiterate something about all these nutrient deficiencies: I’m not talking about acute deficiencies, for the most part. You’re not going to end up in the ER with a deathly case of hypokalemia (potassium deficiency). You probably won’t get scurvy from a lack of vitamin C, even while crossing the Atlantic on a crusty galleon, nor will you develop goiter because you’re living on foods grown in completely iodine-deficient soils. And yet milder, somehow more pernicious deficiencies of these nutrients are a real possibility, even among Primal eaters. These are the symptoms that “everyone has,” that are “just part of getting old.” Bad lipids, fatty liver, fibromyalgia, constipation, general fatigue throughout the day – these are the new normal. But because you’re clued in to the state of your body, and you’re not just going through the motions and accepting the “fact” that you’re going to feel like crap most of the time and it’s all out of your control, you notice when things are off. When you notice something’s off, you explore the literature for clues and nutrient interactions and potential deficiencies. And you’ll often find them.

You’re not alone. Plenty of people on the Standard American Diet are deficient in many or all of these nutrients; they just don’t know it, and they never know to test for it. If they’re lucky, they find out they have fatty liver, but their doctor never mentions choline. Their kids might have asthma, but they hear nary a peep about manganese. They’re put on thyroid medication immediately, without exploring iodine and selenium supplementation. They’re developing osteoporosis, and the only nutritional intervention the doctor considers is calcium, before turning to the drugs. There’s no mention of other trace minerals.

Though it may force you out of your comfort zone, the heightened awareness of nutrients and their roles in health and disease is ultimately a good thing. Embrace it.

Well, that about wraps it up. If I’ve made an egregious omissions from this short series of posts, be sure to let me know in the comment section. Thanks for reading!

About the Author

Mark Sisson is the founder of Mark’s Daily Apple, godfather to the Primal food and lifestyle movement, and the New York Times bestselling author of The Keto Reset Diet. His latest book is Keto for Life, where he discusses how he combines the keto diet with a Primal lifestyle for optimal health and longevity. Mark is the author of numerous other books as well, including The Primal Blueprint, which was credited with turbocharging the growth of the primal/paleo movement back in 2009. After spending more than three decades educating folks on why food is the key component to achieving and maintaining optimal wellness, Mark launched Primal Kitchen, a real-food company that creates flavorful and delicious kitchen staples crafted with premium ingredients like avocado oil. With over 70 condiments, sauces, oils, and dressings in their lineup, Primal Kitchen makes it easy to prep mouthwatering meals that fit into your lifestyle.

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