Reversing Auto-Immune Disease and Healing the Thyroid

NOTE: This information should never take the place of guidance from a medical doctor and is intended for reference. Please consult with your physician, a biomedical doctor, holistic doctor, or a naturopathic doctor. Do not adjust or change your medications without consulting with your attending physician. 

The ill-health of our thyroid is one of our first major warning signs that something is drastically wrong and we need help. It is basically screaming for immediate attention due to a toxic overload. Genetically some of us are more prone to this then others. Then there is the EBV factor. Above and beyond that, the other factor commonly overlooked is an overgrowth of parasites. Ironically, Auto-Immune Diseases have one very common root cause, and it centers around the health of our gut. Gut health is linked to the activity of our methylation cycle, which is influenced by our diet, environment, and gene mutations. Beautifully, that means that if we focus on healing our gut by optimizing our methylation cycle, auto-immune responses will improve and/or stop.

If you happen to be one of the 50-60% of the population carrying the MTHFR Gene Mutation (or any other mutation of the methylation cycle), you are at a much higher risk to run into problems with your immune system, thyroid, gut health, IBS, Crohns, etc. simply because age, stress, and an over toxic system (pesticides, hormones, heavy metals, etc) triggers these mutations to become active. But it doesn’t stop there. Other mutations of the methylation cycle exist and are very common. They can hinder your ability to make B12 and D3 which has a whole list of other very aggressive and daunting side effects! (Note a B12 deficiency can also give you hypothyroid symptoms and alter your blood work to the point that you are diagnosed as such.) You can read more about the MTHFR Gene Mutation from Wellness Mama and the Global Healing Center (along with hundreds of other sites). Dr. Amy Yasko’s Genetic Bypass is the ultimate guide to understanding all of this if you’re interested in a textbook explanation with published data to support info presented. Note: Ignoring an active mutation is now considered to bring you to a slow death through numerous auto-immune diseases, ultimately resulting in Alzheimer’s, dementia, MS, and the like.

The cheapest way to acquire your genetic information regarding the methylation cycle mutations is to order an ancestry test kit from ($99). When your results are ready, download the raw data to your computer. Then visit KnowYourGenetics and follow the steps for generating a methylation report. This report is very thorough, includes suggested resources for you to read that will accompany your report, and includes a list of suggested supplements. (Note: You will not need all of these supplements. You should, however, use this list as a reference guide for when you and your physician determine a supplement is needed.) Be sure to discuss your report with your general practitioner. Also make sure to invest time into understanding your results and make sure your future blood work and prescribed medications support your needs. If your doctor doesn’t understand your report or how your dietary choices, lifestyle, supplements, and prescriptions influence your methylation cycle, find a new doctor. Note: Currently there is not a test to determine if your gene mutations are active, BUT there are homocysteine/B12/D3 levels that can be monitored through blood work that should cue medical doctors to a hindered methylation cycle. You too should be watching these levels and requesting copies of your blood work. Don’t be afraid to ask your doctor about low/high levels.

Learn more about the MTHFR and other Methylation Cycle Gene Mutations.

EBV – Epstein-Barr Virus
The Mysteries of the Thyroid by explains the EBV factor. Whether or not you take time to be tested for this, it’s safe to assume we are carriers and to make choices with our lifestyle accordingly. Read the Goop article top to bottom. It’s important.

The remaining factor is parasite overgrowth. It’s pretty much assumed we all live with them. We’re their host. It’s just a fact. BUT, if you should develop an overgrowth, then everything will get way out of hand and the thyroid is yet another big indicator, as are hives, migraines, diarrhea, IBS, etc. Natural Endocrine SolutionsDr. Hagmeyer Explains How Parasites Could Be Making You Worse, and the Thyroid Pharmacist are decent resources that touch on this topic.

Diet – It’s Critical
Our diet plays a huge role in all of this, and everyone’s body tends to have different needs. Genetics play a big role here, as does our lifestyle. Those with the fastest healing results are using a raw vegan-based diet that focuses on 80% of calories being carbs (fresh fruit, fruiting veggies, and greens), 10% of calories being protein (which is naturally in the produce), and 10% being fat (also naturally in the produce). However, some may not be able to jump into a fully raw diet or a fully vegan diet right away due to food sensitivities, gut inflammation, digestive issues, histamine reactions, etc. Because this is such a huge change, many transition with a mix of 80/10/10 raw and the Raw Til 4 diet (which has you eating raw all day long and then a cooked meal in the evening that still fits in the 80/10/10 ration). It is important to realize that eating processed or cooked food will slow down the healing process, so continuously aim for more raw. You can find these diet books at the book store and library. They follow the same guideline as the Alkalizing Cleanse, a complimentary  text to the 80-10-10. For others, they may need to start on a juice diet to under the guidance of a naturopath before introducing whole foods.

If a plant-based diet is not suitable for your lifestyle, consider exploring Andy Cutler Chelation, requesting inflammation/immunoglobulin tests (IgG and IgA), and adopting an auto-immune diet (free of gluten, soy, dairy, nuts).

Another wonderful textbook style reference for understanding general nutrition and health is The China Study. It summarizes decades of nutrition research and helps the common person understand the basic connection between fats and proteins, and our health. You can also watch the Plant Pure Nation on Netflix for a summary of the book.

Why is the raw vegan diet the optimal diet for reversing auto-immune disease and a sick thyroid?

1. Genetics– The 80/10/10 diet is based around foods that are low in methionine. It turns out that MTHFR individuals with an active mutation are actually poisoned with high levels of methionine. Their bodies cannot actually digest it which slows down or stops their methylation cycle. This in turn leaves them extremely tired, struggling with inflammation, and their key organs working too hard to try and process through the methionine overload. In addition, any synthetic form of folate, known as folic acid, that is consumed (from supplements, protein shakes, or enriched in our foods) is also a poison, with the ability to completely stop the methylation cycle. If you’re going to eat foods high in methionine and you are actively mutating, you will need a prescription strength methylfolate or folinic acid to balance the overload of methionine. (BEWARE: Medical doctors who are aware of MTHFR are currently being taught to treat it with the prescription methylfolate instead of focusing on the patient’s methionine intake.) A bonus factor is that low methionine diets are used to starve cancer, and slow down/reverse Alzheimer’s, MS, fibromyalgia, cycts/tumors, Crohns, IBS, etc. If you’re curious about the methionine levels in the foods you eat, a quick search on the internet will help you evaluate this. You can also reference this site.

2. EBV – The Mysteries of the Thyroid explains how to kill the EBV via diet and supplementation. This is very important to factor, and if you get to the end of the article you’ll see they are removing high methionine foods (though meat was not mentioned), processed foods, and adding low methionine foods and supplements. (Note: Some physicians claim 90% of us live with EBV. While come are symptomatic, others are not. It can be managed holistically and nutritionally.)

3. Parasites – The most effective way to rid yourself of parasites and an overgrowth is by creating an internal environment that is not a friendly host for them. The more alkaline you can be, the less you are a host. Thus why people are successful with the Alkalizing Cleanse approach. The 80/10/10 diet, if followed raw or almost entirely raw, will help you achieve that. Cooked foods, animal foods, and processed foods are actually digested as acidic, which is a perfect host for the parasites you are trying to get rid of. Removing those foods will kill them slowly. To learn more about parasites and their role in our health, listen to lectures at

Regardless of which factor(s) listed above is/are causing your auto-immune disease and sick thyroid, all of them respond well when treated with a low methionine diet. It is also commonly suggested to remove as many environmental toxins and exposure to pollutants as possible. This means eating organic and fresh/unprocessed foods, avoiding any food contact with aluminum and plastics, drinking filtered water (reverse osmosis/distilled), avoiding alcohol, dairy, wheat/gluten, oats, oils, meat, eggs, soy, sugar/artificial sweeteners, soda, bottled juices, caffeine, etc., switching your laundry detergent and hygiene products to natural ones (including deodorant), etc. Baking soda and vinegar are amazing substitutes for household cleaners, shampoo and conditioner, and cleaning the laundry. Remember, anything you do to help rid your home and body of toxins will help. Do what you can and try not to stress about what you can’t.

A very simple daily diet approach:
Breakfast: 48-64 oz fruit smoothie or fruit salad (3 frozen ripe bananas, berries, and sweet fruits)
Lunch: 1-2 heads of romaine, 1.5 lbs tomatoes, 2 bell peppers, 1 cucumber, 3 stalks celery, and an 18 yr aged Italian balsamic for a dressing (Adding up to half an avocado or 5 olives is compliant with the ratios, if desired.) *Feel free to use your favorite fruiting and root vegetables.
Snack: 1 melon or 4 bananas and 2 apples (or large fruit salad)
Dinner: another salad or something cooked (lentil pasta with marinara and 2 cups of steamed peas; homemade vegan vegetable soup; rice and black beans with a salad; taco salad; baked potatoes and salad or steamed veggies)
Evening Snack: more fruit like the last snack

Keep in mind, the best food sources for cleansing the colon and healing your gut are juicy ripe melons and spotted ripe bananas. When in season, aim to eat a melon a day. Because bananas are readily available year round and are easy to purchase, they are the perfect go-to food source. Aim to eat 5 to 10 bananas a day.

Calorie goal is typically recommended at 2000-2500 calories, daily. Use to help track  nutrients. Adding zinc to the morning smoothie will help balance your copper and zinc ratios. A liquid B12, taken first thing in the morning is highly recommended. Some eat a Brazil nut for Selenium. A D3 supplement is also important for most. Spirulina may be of interest too. Lastly, and perhaps most importantly, a strong probiotic (50-80 billion cultures) and 500 mg L-glutamine (taken together) are needed to help heal the gut.

Remember, the goal here with all of this is to heal the gut. An alkaline diet combined with these supplements will help you heal quickly. Your adrenals will be the first thing to heal, and once they are clear, your liver and kidneys will begin to detox too. Other forms of assisting your body in detoxing from heavy metals and environmental toxins is discussed here.

Additional Resources:
Hypothyroid Mom
America’s Thyroid Epidemic
The Global Healing Center
Fruiting Healing
Raw Food Romance