Everyone has bacteria in their digestive tract, or gut, that is essential to the function of the human body. A healthy adult has about 1.5 – 2 kg of bacteria in their gut, both good and bad.  Normal levels of bacteria, or flora, in the gut protect against invaders, undigested food, toxins, and parasites. When the good and bad bacteria in the gut get out of whack (i.e. more bad than good), a whole host of negative reactions can occur in the body.  Undigested foods can leak through into the bloodstream causing food allergies and intolerances, vitamins and minerals may not be absorbed, leading to deficiency, and the bad bacteria can produce a whole host of toxins, leading the immune system to not function properly. An effective thyroid diet includes probiotics that you can get from fermented foods.
This can lead to low T3 levels (58). In addition, elevated cortisol will cause thyroid hormone receptor insensitivity meaning that even if T3 levels are high enough, they may not be able to bind normally to receptor sites. And when this happens it doesn’t get into the cells.  Cortisol will also increase the production of reverse T3 (rT3), which is inactive (11).
Stress can also be caused by chronic digestive issues. When the small or large intestine is in distress (ywhen you are always constipated, bloated, suffer from gas, pain, loose stool etc.), the body sees it as a state of stress. Cortisol is a potent hormone we won’t function without. However, when in excess, it can have a detrimental impact on the thyroid and the immune system (one of the functions of cortisol is to modulate the immune system).
Why does this happen? The immune system mistakenly thinks that the thyroid cells are not a part of the body, so it tries to remove them before they can cause damage and illness. The problem is that this causes widespread inflammation, which can result in many different problems. According to Dr. Datis Kharrazian, 90 percent of people with hypothyroidism have Hashimoto’s that inflames the thyroid gland over time, but this isn’t the only cause of hypothyroidism.
Rather than giving Synthroid (T-4) alone, Dr. Weil prefers combinations of the two natural hormones (T-3 and T-4), and often recommends the prescription drug Thyrolar. Under normal conditions, the body can convert T-4 into T-3; however, there is some question whether the body can do this optimally when under extreme physical or emotional stress. Giving a combination seems to elicit a more natural response for the body, and may also have a better effect on mood than T-4 alone.
If for some reason the pituitary gland or the hypothalamus are unable to signal the thyroid and instruct it to produce thyroid hormones, it may cause decreased T4 and T3 blood levels, even if the thyroid gland itself is normal. If pituitary disease causes this defect, the condition is called "secondary hypothyroidism." If the defect is due to hypothalamic disease, it is called "tertiary hypothyroidism."

You may find that changing your diet will help. One suggestion is to reduce or eliminate sugar, limit fruit, dairy, and grains, and get your carbohydrates mainly from vegetables. Round out your diet with lean proteins and healthy fats. In addition, eating two to three meals a day, no snacks, and avoiding food after 8 p.m. seems to help balance hunger hormones and blood sugar—and promote fat burning. 
Thyroid hormones regulate cholesterol synthesis, cholesterol receptors, and the rate of cholesterol degradation. Hypothyroidism increases LDL levels, and increased cholesterol levels have been shown to induce hypothyroidism in animal models. Normalization of thyroid hormone levels has a beneficial effect on cholesterol, which may be worth noting especially for clients who choose not to take prescribed thyroid medications.7
Getting enough fiber is good for you, but too much can complicate your hypothyroidism treatment. The government's Daily Guidelines for Americans currently recommends that older adults take in 20 to 35 grams of fiber a day. Amounts of dietary fiber from whole grains, vegetables, fruits, beans, and legumes that go above that level affect your digestive system and can interfere with absorption of thyroid hormone replacement drugs.

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Please Note: The material on this site is provided for informational purposes only and is not medical advice. Always consult your physician before beginning any diet or exercise program.

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