Micronutrient Deficiencies (Part 1 of 2)


Micronutrients are important for proper thyroid function

Hypothyroidism affects nearly 10% of the US population. That’s upwards of 35 million people. And Hashimoto’s is believed to be the leading cause.

In actuality, hypothyroidism can be caused by many other factors, as well. And to complicate matters, both of these conditions can lead to the other.

Prolonged, chronic hypothyroidism can become Hashimoto’s and virtually everyone with Hashimoto’s becomes hypothyroid eventually because their thyroids are gradually destroyed by their immune system.

Nutrient Deficiencies are a Common Factor

One common factor that we see with both patient populations is deficiencies of important micronutrients such as selenium, zinc, iron, Vitamin D, B Vitamins, Vitamin A and Vitamin E.

(Iodine is also an important nutrient that is sometimes deficient, but it is also quite controversial due to it’s ability to rapidly cause an increase in both TSH and antibody levels, and in some cases, increase in hypothyroid symptoms. People with Hashimoto’s, MUST, therefore be extra cautious hen supplementing with iodine. As a general rule you should test first, then, if you need to supplement, work with someone who knows what they are doing.)

In this 2 part post we will first explore some of the causes of nutrient deficiencies, and, then in part 2, best practices for supplementing and correcting them. And of course, as always, why it matters.

What Causes Nutrient Deficiencies?

If you are a follower of our blog, you know that I’m always interested in why things happen, so before we look at the actual nutrients, let’s look at the most common causes of nutrient deficiencies in the body.

1. Low Stomach Acid
2. Leaky Gut or Intestinal Permeability
3. Soda Consumption
4. Tea and Coffee
5. MTHFR and VDR Gene Mutations

Low Stomach Acid: A Bigger Problem Than You Think

With Hashimoto’s and hypothyroidism, a very common problem is that too little gastrin and stomach acid (hydrochloric acid or HCL) are produced. This can result in a number of things that can lead to micronutrient deficiencies.

(For an in depth read on this problem, check out this post.

For example, one thing that HCL is important for is the absorption of vital nutrients like B12, iron, and calcium and for breaking down and absorbing protein.

Too little HCL can also lead to inflammation, lesions and infections in the intestines.

All of that leads to poor absorption of these nutrients and thyroid hormone, leading to a vicious cycle that leads to more hypothyroidism and more nutrient deficiencies.

It’s a positive feedback loop of repeated deficiencies making each other worse.

The following micronutrients depend on proper stomach acid levels in order to be absorbed in the small intestine:

Selenium (selenite form is not pH dependent)
B 12

And it’s also important to note that medication that reduces and/or eliminates acid reflux like proton pump inhibitors and antacids, may also cause poor absorption of these vitamins and minerals.

Leaky Gut or Ground Zero for Autoimmunity

When the lining of the digestive tract is inflamed, the connections between the pieces of lining known as “tight junctions” break down and allow large, undigested compounds—toxins and bacteria—to leak into the bloodstream.

These substances all react with the intestine’s immune system and cause an exaggerated immune response. This over-reaction by the immune system becomes another vicious cycle that leads to more intestinal damage.

And as this problem grows, diet, lifestyle, medications, and infections can cause further intestinal inflammation that can ultimately lead to more serious problems.

In addition, after the intestinal lining becomes damaged, the damaged cells become unable to properly digest food and produce the enzymes necessary for digestion.

How Damage Leads to Micronutrient Deficiencies

This damage can lead to micronutrient deficiencies, malnourishment, hypothyroidism and more autoimmune disease.

It’s another positive feedback loop perpetuating further damage and further deficiencies. This is a problem because so many things are absorbed in the gut, mostly through the small intestines.

For example:

Approximately 80% of water is absorbed by the small intestine, 10% by the large intestine and the remaining 10% excreted in the feces.

All of the important electrolytes are absorbed in the small intestine: chloride, iodine, calcium (these are absorbed with the help of vitamin D), iron, magnesium and potassium.

Vitamins including fat soluble ones (Vitamins A, D, E and K) are absorbed together with dietary fats.

Water soluble vitamins like vitamins B and C are absorbed by diffusion. Vitamin B12 combined with intrinsic factor (from the stomach) is absorbed by active transport.

Of these iron is absorbed in the duodenum, most are absorbed in the jejunum and Vitamin B12 and bile salts are absorbed in the later part of the ileum.

So you can see, when this process is damaged or impaired there are a lot of potential consequences.

What Micronutrients Are Not Absorbed?

There are several micronutrient deficiencies that a recent Brazilian review published in 2012 by Teixeira TF et al found to be associated with leaky gut and obesity, specifically vitamin A, magnesium, zinc, vitamin D, and calcium.

Vitamin A, zinc, and magnesium all help maintain tight junctions in the intestine and regulate endothelial cells in the gut, while vitamin D stimulates intestinal lining rebuilding and it can slow the damage by calming and regulating the immune system.

Vitamin D and calcium play a joint role in maintaining the protective barrier of the intestines by helping ATP (the cell’s energy source) mechanisms in the intestinal cells.

In obesity (which is found in some hypothyroid and Hashimoto’s patients), intake of these micronutrients is sometimes low, so deficiencies could play a major role in making leaky gut conditions worse, especially when combined with an unhealthy intestinal  ecosystem and poor food choices.

What that all means is that having a good intake of these micronutrients could be protective against the development of leaky gut and the inflammation and eventual obesity it can cause.

Soda: Sugar, Caffeine and Phosphoric Acid: A Perfect Recipe for Micronutrient Loss

Most popular sodas (like Coke, Pepsi, Dr. Pepper and Mountain Dew, etc.) are loaded with sugar, and caffeine and this mixture is suspended in phosphoric acid, which actually allows you digest it.

Here’s what happens in your body when you drink one of these drinks:

First, about 10 teaspoons of sugar hit your system (roughly 100% of what you’re supposed to consume in a day). This causes a massive spike in insulin and your liver freaks out and turns all of this excess sugar immediately into fat.

Then the caffeine kicks in and causes a massive burst of stress hormones to be released from the adrenals, which causes the liver to kick all that sugar into your bloodstream and causes a massive release of cortisol to try and deal with it.

This cortisol release also reduces stomach acid levels, impairs your immune response and, ultimately, causes your intestinal lining to be further compromised.

Sugar, caffeine and phosphoric acid all impair absorption of vital nutrients like iron, calcium and zinc. And the phosphoric acid actually binds to these minerals.

Then the diuretic properties of caffeine kick in and you pee all these valuable nutrients out.

Coffee, Tea and Bye Bye Micronutrients

This is pretty much the same as soda, minus the added problems caused by phosphoric acid.

Let’s take a look at how caffeine can lead to deficiencies in important micronutrients.


As we discussed above, caffeine is a diuretic. It makes you pee. Caffeine causes calcium to be excreted in the urine and feces. According to “Effects of caffeine on health and nutrition: A Review” by Tsedeke Wolde,  for every 150 mg of caffeine ingested, about the amount in one cup of coffee, an estimated 5 mg of calcium is lost.

Caffeine also inhibits the amount of calcium that is absorbed through the intestinal tract and depletes the amount retained by the bones. In fact, one study of postmenopausal women found that those who drank more than 300 mg of caffeine lost more bone in their spines than women who did not drink as much.

Vitamin D

Caffeine also inhibits vitamin D receptors, which means less may be absorbed. Because vitamin D is important in the absorption and use of calcium in building bone, this could also decrease bone mineral density, resulting in an increased risk for osteoporosis.


Caffeine interferes with the body’s absorption of iron (sugar does too), which is important for many processes in the body like red blood cell production, and carrying thyroid hormone to the cells.

Tea reduces iron absorption significantly more than coffee, but both impair absorption. Tannins in tea can also bind to iron, and prevent absorption of calcium and thyroid hormone, as well.

B Vitamins

Water soluble vitamins, such as the B-vitamins, can be depleted by the fluid loss caused by the diuretic effects of caffeine. In addition, it interferes with the metabolism of some B-vitamins, such as thiamine (vitamin B1).

Caffeine may also reduce the absorption of manganese, zinc and copper. It also increases the excretion of the minerals magnesium, potassium, sodium and phosphate. There is also evidence that caffeine interferes with the action of vitamin A.

MTHFR and VDR Gene Mutations: Not Helping Matters

Basically, what the MTHFR gene does is produce an enzyme with the same really long name (methylenetetrahydrofolate reductase).
Genes produce enzymes and these enzymes do all the heavy lifting, they do the work.

Without enzymes we wouldn’t have physiological function.

The job for the MTHFR enzyme is to convert one form of folate into the most active and usable form of folate in the human body – in every cell in the body. This type of folate is called methyltetrahydrofolate  or more commonly by it’s nickname methylfolate.

Another really common finding that I see in analyzing blood test results from Hashimoto’s patients is that they have high levels of homocysteine.

As it turns out, low activity of the MTHFR enzyme may also lead to this. High homocysteine is a major risk factor for heart disease, inflammation, difficult pregnancies, birth defects, and more.

Nutrient deficiencies in Folate B6, and B12 have been linked to high homocysteine.

To matters more complicated, people with MTHFR issues may have a difficult time processing certain types of folic acid like those found in processed food and cheap supplements.

VDR gene defects can lead to poor absorption and utilization of vitamin D in the body, which can lead to a more active immune system, worse symptoms and a faster progression of Hashimoto’s and hypothyroidism.

You see, more positive feedback loops resulting in more vicious cycles reinforcing an existing problem.

A Perfect Storm of Positive Feedback Loops

The big takeaway here is that all the factors mentioned in this article can lead to positive feedback loops or repeated problems that make each other worse. So if you have low stomach acid, leaky gut and you drink sodas, coffee and tea, you may be, unwittingly, causing your own health to decline.

And in this situation, taking supplements containing these vitamins and minerals may not do much good if you don’t address the root causes of the problems  (like the low stomach acid and leaky gut) and start working on reducing the positive feedback loops that lead to this in the first place.

Because here’s the thing, these positive feedback loops can be reversed and you can achieve positive healing momentum if you get to the bottom of this and correct the underlying imbalances. I write all about how to do this in my new book, Roadmap to Remission.

In part 2 of this post, we’ll explore these micronutrients and look at best practices for correcting the causes of deficiencies and for supplementing them with food and supplements.


http://www.ncbi.nlm.nih.gov/pubmed/18341376 -Coffee interferes with T4 absorption

Benvenga, S. et. al. “Altered Intestinal Absorption of L-Thyroxine Caused by Coffee.” Thyroid. Volume 18 Issue 3, pages 293-301. March 2008 Abstract.

Mazzaferri, MD MACP, Ernest. “Thyroid Hormone Therapy,” Clinical Thyroidology for Patients: Summaries for Patients from Clinical Thyroidology. August 2008 Vol 1, Iss 1.

Sindoni, Alessandro et. al. “Case Report: Coffee Impairs intestinal Absorption of Levothyroxine: Report of Additional Cases,” Hot Thyroidology, Article 5/09

http://www.ncbi.nlm.nih.gov/pubmed/23039890 – Severity of Hashimoto’s corresponds with genetic defect

http://www.ncbi.nlm.nih.gov/pubmed/17669709 Effect of proton pump inhibitors on absorption of levothyroxine


http://www.ncbi.nlm.nih.gov/pubmed/23084636 Obesity and nutrient deficiencies linked to leaky gut


http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2084394/ -Intestinal crosstalk, very interesting article on how this is all connected

http://www.ncbi.nlm.nih.gov/pubmed/7599455 caffeine and calcium

http://www.ncbi.nlm.nih.gov/pubmed/1564564 calcium, coffee and oesteoporisis

http://www.ncbi.nlm.nih.gov/pubmed/16758142 Swedish cohort on oesteoporosis and caffeine

http://www.ncbi.nlm.nih.gov/pubmed/6402915 inhibition of food iron by coffee

http://www.ncbi.nlm.nih.gov/pubmed/6896705 Effects of various drinks on iron absorption

Effects of caffeine on health and nutrition: A Review, Tsedeke Wolde Lecturer of Nutrition, Department of Public Health, College of Medical and Health Sciences, Wollega University, Nekemte, Ethiopia

The Thyroid, A Fundamental and Clinical Text, Ninth Edition. Lewis E. Braverman and Robert D. Utiger 2005


About the Author Marc Ryan

So now, not only is it my profession, it’s my passion, and it’s personal. I’ve been joking with people lately saying it’s a blessing and a curse. A blessing because I really get it, and a curse because I really got it! ?

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