1. Jonklaas J, Bianco AC, Bauer AJ, Burman KD, Cappola AR, Celi FS, et al. American Thyroid Association Task Force on Thyroid Hormone Replacement. Guidelines for the treatment of hypothyroidism: prepared by the American Thyroid Association Task Force on Thyroid Hormone Replacement. Thyroid. 2014;24:1670–1751. [PMID: 25266247] [PMC free article] [PubMed]
Hypothyroidism is a disease which causes the thyroid gland to become underactive and not making enough thyroid hormones. The thyroid gland is located in the front lower part of your neck. Hormones released by the gland affect nearly every part of the human body including heart, brain, muscles, and skin. The thyroid controls the metabolism, which affects the body temperature, heartbeat and also regulates the calorie burn. When the body is unable to produce enough thyroid hormone, it causes the metabolism to slow down and hence, the body makes less energy and gain more weight. 
If your sex hormones (estrogen, progesterone, testosterone) and adrenal hormones (cortisol, DHEA) are out of balance, this can make weight loss more difficult. Perimenopause and menopause, as well as estrogen dominance, can also cause a shift of weight to the belly, and make weight loss more difficult. Lack of testosterone in men and women can also make it harder to build fat-burning muscle. And adrenal imbalances can make you tired, less responsive to thyroid treatment, and less able to lose weight.
Soy? If you have hypothyroidism, yes. Eating too much soy causes problems only for those with hypothyroidism, which occurs when your thyroid gland does not make enough thyroid hormones, Dr. Nasr says. The main problem is that soy hinders absorption of the hormones such patients are taking. “Some studies show that if you eat a lot of soy, or drink a big glass of soy milk, within one hour of taking a thyroid hormone, it might affect absorption,” he says. “A lot of people depend on those hormones to achieve a steady state.
8)  Supplement With Omega 3’s:  Omega 3 fatty acids and in particular the long chain variety EPA and DHA are critical for stabilizing blood sugar, reducing inflammation and taming the immune system.  Consume grass-fed meat, grass-fed butter, wild-caught fish and spirulina to get it in your diet. It is also advisable to supplement with 2-5 grams daily of EPA/DHA along with 200 mg of GLA.  Clinically, I use ProEFA to boost up omega 3’s.

First things first, you must consider food to be your medicine and get off all processed junk food, sugar (which sends you on a hormonal rollercoaster ride) and gluten. The Daily Living Eating Plan is a great place to start. In addition, l-glutamine is a key amino acid that reduces cravings for high-glycemic carbohydrates and helps kick the sugar habit. If you have already done that and are looking to go deeper, here are some tips to heal the thyroid:

l-Thyroxine monotherapy, the novel and physiologically savvy method for treatment of hypothyroidism, contrasted with the traditional approach of natural thyroid preparations that was marred by potency concerns. In less than a decade, there was a major shift in treatment of hypothyroidism such that normalization of TSH with l-thyroxine monotherapy became the new standard of care (Appendix Table) (52). Many clinicians advocated for this to be first-line therapy and for patients previously treated with desiccated thyroid to be transitioned to l-thyroxine monotherapy (50).
*Cassava bears special mention here.  You may have heard of it because it is the starchy root vegetable from which tapioca is made, but cassava is also a popular staple food in many Third World countries, where it is eaten boiled, mashed, or ground into flour.  Fresh cassava root contains a harmless substance called linamarin, which can turn into hydrocyanic acid (aka cyanide!) when the plant is damaged or eaten. Flaxseeds also contain linamarin. Cyanide is very toxic, so the human body converts it into thiocyanate (which, although it does interfere with thyroid function, is less toxic than cyanide and easier for the body to eliminate).
Diagnosis of hypothyroidism is based on your symptoms and the results of blood tests that measure the level of TSH and sometimes the level of the thyroid hormone thyroxine. A low level of thyroxine and high level of TSH indicate an underactive thyroid. That's because your pituitary produces more TSH in an effort to stimulate your thyroid gland into producing more thyroid hormone.
Thus, neither desiccated thyroid nor l-thyroxine monotherapy recreates a biochemical state of euthyroidism as defined by the serum T4:T3 ratio. l-Thyroxine and l-triiodothyronine combination therapy theoretically could be titrated to restore this measure, but such a method would be challenging because of the frequent dosing schedule needed to achieve stable serum T3 levels (5). New technology is needed to allow for steady delivery of l-thyroxine; only then would high-quality clinical trials best investigate the utility of the serum T4:T3 ratio as an outcome measure in hypothyroidism.
Vitamin D is important for immune system health and is made in the skin from exposure to the sun's ultraviolet rays. Vitamin D is also found in foods like fatty fish, cod liver oil, and fortified cereals. Research suggests that vitamin D deficiency may be linked to the development of Hashimoto's thyroiditis (autoimmune hypothyroid disease), and that vitamin D supplementation may help with the treatment of thyroid disease.  
Correcting these problems requires an integrative approach. It involves more than simply taking a thyroid pill. As you’ll see, it involves nutritional support, exercise, stress reduction, supplements, reducing inflammation, and sometimes eliminating certain foods and detoxification from heavy metals (such as mercury and lead) and petrochemical toxins (such as pesticides and PCBs).
High-fat fried foods, like mozzarella sticks, jalapeno poppers and um…fried chicken and French fries can contribute to inflammation in the body, says Blum. Inflammation from Hashimoto’s disease, also known as chronic lymphocytic thyroiditis, often leads to an underactive thyroid gland. Hypothyroidism primarily affects middle-aged women, according to the Mayo Clinic, but it can target anyone at any age.
Most people with hypothyroidism don’t need to steer clear of soy completely. But it’s a good idea to limit your consumption to a few servings a week, and to stick with minimally processed forms of soy like tempeh or miso. Foods containing processed soy protein isolates (like soy protein powder, soy protein bars, or soy-based meat analogs) tend to have a higher concentration of isoflavones, says Markley.
55. National Cholesterol Education Program (NCEP) Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (Adult Treatment Panel III) Third Report of the National Cholesterol Education Program (NCEP) Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (Adult Treatment Panel III) final report. Circulation. 2002;106:3143–3421. [PMID: 12485966] [PubMed]
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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