How We Become Selenium Deficient
Selenium deficiency is not thought to be common in healthy adults, but is more likely to be found in those with digestive health issues or chronic inflammation causing poor absorption of nutrients. 
So people with Celiac, Crohn's, IBS, IBD and other autoimmune conditions are at higher risk of becoming selenium deficient. 
The most common cause in a modern world is going to be digestive dysfunction.
What are some mechanisms that could underly digestive dysfunctions?
Almost all digestive disorders share one or more of the following underlying mechanisms:
- An overgrowth of bacteria in the small intestine
- Dysbiosis or imbalance between “good” and “bad” microbes in the gut
- A permeable gut barrier (leaky gut)
- Chronic bacterial, parasitic, or fungal infections (such as pylori, Blastocystis hominis, Candida albicans)
- Low stomach acid or digestive enzyme production
- Sensitivity, allergy, or intolerance to certain foods
- Impaired communication between the gut and the brain
In my opinion and regardless of symptoms, I believe that everyone should be working towards optimizing gut health simply because it plays such a strong role in overall health. The reality is that you can be eating enough selenium through food, but if there is something blocking or inhibiting absorption, then you could develop a deficiency.
I'd like to make it clear that scientists don't believe selenium deficiency itself causes disease, but makes the body more susceptible due to it's role in immune functions.
Adequate selenium nutrition supports efficient thyroid hormone synthesis and metabolism and protects the thyroid gland from damage from excessive iodine exposure.
Let's talk more about that…
The Link Between Selenium & Hypothyroidism
Selenium is an important trace element and antioxidant required for healthy thyroid hormone synthesis and metabolism.
The thyroid gland has been found to have the highest content of selenium per gram of tissue among all the organs in the human body. 
Selenium supports the conversion of your body’s inactive thyroid hormone thyroxine (T4) into the form your body needs, the biologically active triiodothyronine (T3). 
As I've discussed in other articles, thyroid physiology is complex and there are several mechanisms that the body uses to activate and deactivate thyroid hormone.
One way to put the breaks on your metabolism is to shunt T4 to Reverse T3. You can think of reverse T3 as your active thyroid hormone being in hibernation.
This is important because some selenoproteins can inactivate thyroid hormones increasing the conversion of T4 to reverse T3.
This is why we don't want to blindly increase supplements just because we know they can help.
Selenium also has protective effects acting as antioxidants and protecting our cells from oxidative damage. 
All of the information I just shared is important to understand when it comes to selenium and thyroid health.
In other words, if you don't have adequate amounts of selenium, then the process of creating thyroid hormone can become toxic and initiate hypothyroidism and autoimmune hypothyroidism.
If selenium acts as an antioxidant during T4 to T3 conversion, then deficiencies of selenium result in increased oxidative damage and inflammation within the thyroid tissues!
This inflammation triggers lymphocytes and white blood cells to going on the defense.
As the WBCs begin to attack, small amounts of antibodies are formed to help mark the damaged cells that need to be cleaned up.
In instances of higher turnovers of cells seen with excess oxidative damage due to iodine excess and selenium deficiency, more antibodies are produced and an immune system shift can be induced, resulting in the failure to distinguish self from non-self. 
This is how autoimmunity can start due to a selenium deficiency.
After autoimmunity occurs, the T4 to T3 conversion continues to be impaired.
The decreased production of thyroid hormones due to this impairment results in the stimulation of the hypothalamic-pituitary axis, increasing TSH production.
This in turn stimulates the selenoproteins to convert more T4 and additional oxidative stress is produced. More of it accumulates in thyroid tissue, creating further damage. 
With this understanding, let's talk about how selenium deficiency can occur.
How to Optimize Selenium Levels
So the question you might have is whether or not you should start supplementing with selenium if you have hypothyroidism, Hashimoto’s thyroiditis, or low T3 levels?
If you know that you have a selenium deficiency (because you were tested for it), then you could absolutely benefit from selenium supplementation.
But if you suspect it and don't know for sure, then supplementation could actually make things worse!
Some studies show that there is a U-shaped relationship between selenium concentration in the blood and the risk of disease, with possible harm occurring both below and above the physiological range for optimal activity of some or all selenoproteins. 
High levels of selenium have even been associated with the development of hyperglycemia (high blood glucose) and atherosclerosis. [11, 12]
Let me repeat:
While it seems that selenium supplementation would be an obvious solution to poor thyroid function, long term consumption of high doses of selenium could cause additional symptoms including: gastrointestinal upsets, hair loss, white blotchy nails, garlic breath odor, fatigue, irritability, mild nerve damage. 
For now, the best option for most people may be to include selenium-rich foods in the context of a healthy Paleo diet.
Great sources of selenium include: brazil nuts, crimini mushrooms, cod, shrimp, tuna, halibut, salmon, scallops, chicken, eggs, shiitake mushrooms, lamb, and turkey. F
For those who choose to supplement, I consider 200 micrograms of selenium as selenium-enriched yeast, as found in Thyrotain, as a safe supplemental dose for people with thyroid issues.