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Autoimmune Disease

What Is Known About Autoimmune Disease

Healthy Steps: Autoimmune—First Steps
Healthy Steps: Autoimmune—Full Program
Preventing Autoimmune Disease
From Dr. Deborah's Desk

Next time you have dinner with a group of friends, look around the table: if there are twelve of you, one or two of those present has some form of autoimmune disease. Perhaps three of them, if carefully studied, would have autoimmune antibodies, but not yet have an illness.

If the name “autoimmune illness” seems a little confusing, you are not alone. Each individual autoimmune disease is named according to the part of the body affected, but someone with autoimmune intestinal disease (Crohn’s disease) has a great deal in common with the person with asthma or arthritis , also autoimmune diseases but affecting different body parts. Inflammation is a key part of all of these problems, and the inflammation derives from over-activity in the part of the immune system that produces antibodies to tissues within the body. Our immune system attacks us at home instead of protecting us from foreign proteins of invading bacteria or viruses. 


What Is Known About Autoimmune Disease

Somewhere between 80-100 inflammatory conditions are currently thought to be autoimmune in origin, and the ultimate numbers will probably be even higher. The most common are celiac disease (affecting the small bowel) and Hashimoto’s disease, affecting the thyroid. Other well-known examples of autoimmune illness are lupus, multiple sclerosis, asthma, inflammatory bowel disease, psoriasis, arthritis (Rheumatoid or osteoarthritis), scleroderma, type 1 diabetes, and more; likely autoimmune diseases include ALS (amyotrophic lateral sclerosis or Lou Gehrig’s Disease), fibromyalgia, vitelligo, and possibly chronic fatigue syndrome and diverticulitis. Having one autoimmune disease greatly raises your risk of a second, and while there is clearly a genetic component to autoimmune disease, family history does not fully explain its increased incidence over the last 50 years. 

You will not find a specialist in autoimmune disease if you look in the phone book. Even a very sophisticated medical textbook (such as Alan Gaby’s Nutritional Medicine) groups illnesses according to the organs affected, rather than considering autoimmune disease as a category onto itself. (A current and very complete book on the topic is The Paleo Approach by Sarah Ballantyne, including a full description of the current science on autoimmune disease as well as a comprehensive set of recommendations for self-healing.) Although these are all separately named diseases, they share a commonality of disease mechanism.

Trends in autoimmune disease are fascinating, raising more questions than they answer. More than three quarters of those affected are women, for a start. Autoimmune disease is more prevalent in more affluent countries – and even increased in more affluent neighborhoods!  Autoimmune disease also varies by latitude (less of it near the equator) and by the hygiene of the environment: more primitive areas have less autoimmune disease, farmers have less than city dwellers, while farmers who handle animals (and their manure) have less than farmers who stay out of the barn. When African women were “cured” of their worm infestations during pregnancy, their children had greater incidence of asthma and eczema. Eczema is not classified as autoimmune, but is frequently associated with some form of autoimmune disease, and shares the common symptom of inflammation.  There is clearly some association between inflammation, allergies, and autoimmune disease, but all the particulars have not been well sorted out, although we can make at least three fairly interesting observations.

We each have a unique immune system that is quite complex, and we continue to learn about the different functions of its various components, specifically T cells and B cells. Both kinds of cells can contribute to autoimmune disease, the defining characteristic being that an immune response is amped up in response to a protein living within our own bodies, a protein we should not be considering as foreign. That’s the gas pedal and it gets stuck in the on position. The brake pedal, the protective part of our immune system, is unfortunately overpowered.

Agricultural families or primitive tribesmen relied on that sturdy gas pedal to keep at bay the various invading pathogens that might make them ill. Keeping that sturdy gas pedal in a much cleaner world might create a situation where the gas pedal sees even innocuous proteins, or internal ones, as hazardous and attacks them. For a great read and lengthy discussion of this possibility, see An Epidemic of Absence by Moises Velasquez-Manoff.

Additionally, intestinal permeability coexists with autoimmune disease, and is generally considered essential to its development. When the intestines are extra permeable, the normal “tight junctions” between intestinal cells become open doors and proteins seep into the bloodstream before they are digested into smaller, and less immune provocative, amino acids.

Finally, the increase in severe and life-threatening food allergies parallels the recent increase in autoimmune disease. Recent research has suggested that an antibiotic-scrubbed microbiome might be contributory to severe allergies. In a study at the University of Chicago, intestinal bacteria normally present were returned to mice with depleted intestinal flora, and the mice lost their severe food allergies. The study’s findings raise the possibility that excessive treatment with antibiotics, prescribed for a patient or simply present in the general food supply, might eradicate protective species of bacteria that render the intestine more permeable and increase the tendency to allergy or autoimmune disease.

Once again, we come to the thought that the gut might be a key aspect of health – in this case autoimmune disease – and a possible path to re-balancing the immune system and reducing or eliminating autoimmune disease. Self-care steps can be taken while continuing any conventional medical treatment prescribed for an autoimmune condition. When I work with individuals whose symptoms improve, I suggest they consult with the prescribing physician about the possibility of decreasing prescription medications. 

Healthy Steps: Autoimmune Disease—First Steps

For the greatest health improvement with the fewest steps, do the following:

  • Remove triggers. Remove foods that can increase intestinal permeability, starting with grains, dairy, and legumes. If that sounds radical to you, visit the page on the Paleo Diet. One of the wonderful things about the Paleo movement is the tremendous spirit of invention that has inspired Paleo recipes for even the most unlikely foods. Paleo banana cream pie? No problem, you can find it!
  • Heal existing digestive problems. If you can work with a physician who can help you identify the current state of your digestive tract, that would be your wisest choice. The most healing food is homemade bone broth, made so that it’s rich in gelatin, drink 2 cups daily. If you have symptoms of irritable bowel, indigestion, or constipation, please consult those pages on this website.
  • Diversify intestinal flora. Make sure your intestinal flora is as richly varied as possible. Start with a lactobacillus/bifidobacterium blend such as Microbiome Labs MegaSporeBiotic, one capsule twice daily with or between meals. Follow with a probiotic containing sacchromyces boulardii, such as Floramyces, dosing in the same way.

Healthy Steps: Autoimmune Disease—Full Program

A comprehensive program involves many areas in which action steps can be taken, gradually or all at once. You will be your own most valuable health manager. Some of the suggestions below include flexibility: balance gentleness and honesty with yourself!

Start by following the basic nutrition and healthy lifestyle guidelines, with the following modifications:

Avoid Problematic Foods

  • Generally problematic foods. Consistent with general recommendations for optimal health, eliminate added sugars, vegetable oils, pasteurized dairy, soy, genetically modified and processed foods. Minimize alcohol, and reduce caffeine if you are sensitive or stressed in any way.
  • Eliminate autoimmune triggers.  Start your autoimmune recovery by removing grains, dairy (butter is allowed), and legumes. Although that may sound radical, you can relax knowing that your resolution should be simple.
  • Keep searching for triggers. If you have no improvement after 6 weeks, swap butter out, allowing ghee, and work your way through Sarah Ballantyne’s list of other auto-immune provoking foods, as follows: eggs; nuts; seeds (including chocolate, coffee, and spice seeds); citrus; and nightshades. HOW you eliminate these foods is up to you.  You can choose to
    • Eliminate them all at once and re-introduce foods one at a time (a week apart) to see which are the forbidden-for-you foods OR
    • Eliminate one group at a time, for at least 10 days, before eliminating the next,If you note no improvement after eliminating all these foods, you might want to consult a knowledgeable practitioner to be sure you are not eating anything that might be confounding, despite eliminating the obvious potential problems.

Savor Helpful Foods

  • Keep your diet rich in nutrients. Enjoy a variety of nutrient dense foods in your regular eating patterns: eat the meat and organs (liver, tongue, heart, and more) from pasture-raised animals; shellfish or fish, preferably wild or sustainably raised; a wide variety (eat all the colors) of vegetables and fruits, emphasizing vegetables rather than fruits. Without dairy, you can still enjoy plenty of health fats such as fat that comes naturally with fish or with meat, avocado, coconut, and olive oils. 
    • Seafood: Emphasize omega-3-rich varieties such as wild Alaskan salmon and salmon roe (avoid farmed), herring, anchovies, sardines, and cooked or smoked oysters. To enhance nutrient absorption, add coconut, avocado or olive oil to your plate.
    • Raw fish: To ensure safety, marinate for 7-24 hours in lemon or lime juice.
    • Lamb, beef, and pork: Consume with the fat and avoid overcooking to maintain tenderness.
    • Venison, elk, and bison: These meats may require marinating 3-24 hours for tenderness. Enjoy with butter or coconut cream sauce.
    • Raw meat: Considered a delicacy in traditional cultures, raw meat should be frozen for 14 days to eliminate parasites.
    • Poultry: Enjoy chicken, duck, geese, quail, and Cornish game hens and consume with the skin and fat.
    • Eggs: Consume eggs from pastured hens whenever possible. Eat as many eggs as desired.
    • Organ meats: Eat twice weekly minimum OR find a good organ meat supplement. Primarily available from cows and chickens, organs such as liver, heart, and kidneys are superlative sources of trace minerals and fat-soluble vitamins. Many people find liver unpalatable, but consider this: If you do not eat liver, you will need to find supplements to provide chromium, biotin, inositol, alpha lipoic acid, and other vital nutrients. Mention “paté,” however, and most people will smile. You can also enjoy organs as liverwurst, chopped finely and added to soups and stews, or mixed with ground meat as meatloaf or meatballs. (Pro-tip: pre-soaking the liver in lemon juice results in a milder taste.)
  • Fat: Essential for nutrient absorption, adequate fat also provides satiety in a carbohydrate-cautious diet. Restricting fat is hazardous causes fat-soluble vitamins to be lost and protein content to increase to dangerous levels for the kidneys.
    • Animal fats: Butter (IF you tolerate) or ghee , fatty cuts of meat, poultry skin, and fat reserved from roasting meats provide valuable sources of fuel and fat-soluble vitamins. Use fats only from grass-fed meats. 
    • Vegetable fats: Choose organic fats to avoid oil-soluble residues of chemicals or hormones. Healthy choices include coconut oil, coconut milk, extra virgin unrefined olive oil, and, for flavor, small amounts of sesame oil or other nut oils, unless you are eliminating nuts and seeds. For sautéing, maintain low temperatures and use fats that are solid at room temperature such as coconut oil, butter, ghee, and animal fat.
    • Avocado: Half an avocado daily (at a minimum) provides a tasty fat and a valuable source of healthful fatty acids and nutrients.
    • Nuts. If you have not yet eliminated nuts, it is vital that you confine your nut consumption to nuts prepared according to the crispy nuts recipe!
  • Vegetables: Vegetables provide necessary minerals and phytonutrients. Eat vegetables lightly steamed with butter or ghee and sea salt; or raw in salads with olive oil and vinegar dressing. If you juice your vegetables, drink them with a meal, not instead of a meal. Extra fats aid in nutrient absorption. Bitter greens are especially rich in nutrients. Limit root vegetables as described below.
  • Heal existing digestive problems. If you can work with a physician who can help you identify the current state of your digestive tract, that would be your wisest choice! The most healing food is homemade bone broth, made so that it’s rich in gelatin, drink 2 cups daily. If you have symptoms of irritable bowel, indigestion, or constipation, please consult those pages on this website.
  • Enrich intestinal floraMake sure your intestinal flora is as richly varied as possible. Start with a lactobacillus/bifidobacterium blend such as Klaire Ther-Biotic, one capsule twice daily between or after meals. Follow with a probiotic containing sacchromyces boulardii, such as Floramyces, with or between meals. Food sources of priobiotics are incredibly rich, abundant and diverse. Foods you can make yourself (sauerkraut, kefir, kombucha) or purchase provide good prebiotics and probiotics. 

Vital Supplements

  • Barlean's Fish Oil. 1 Tablespoon daily, taken with meals, provides necessary omega 3's.
  • Dr. Ron's Ultra Pure Liver: For those unwilling to eat liver, supplement with liver pills (6 daily).
  • Your favorite kind of vitamin C. Take 500-1000 mg twice daily. Immune imbalance increases the body's need for vitamin C.
  • Vitamin D: Obtain vitamin D from the sun with 20 minutes of full-body (not just hands and ankles) exposure to midday sun (May to September in northern latitudes). With direct UV exposure, the body can generate up to 20,000 units or more of vitamin D daily. Test your blood level of vitamin D3: the ideal range for healthy people is 40-65 ng/ml; those with health challenges may benefit from higher levels. If sun exposure is not giving you adequate vitamin D3 levels, take DaVinci A, D, and K. Take as needed to normalize blood levels. For most adults that amount is approximately 4000 i.u., daily, or consult your health care professional for individual requirements
  • Metabolic Maintenance L-Glutamine comes in either capsules or powder; the dose is 500-3000 mg three times daily with meals.
  • Magnesium Glycinate: Take 150-600 mg daily according to bowel tolerance of this or other healthy magnesium supplement. You can also find magnesium in green leafy vegetables, nuts, seeds, and fish, although even organic soils are thought to be depleted now. Use a topical magnesium (oil or lotion) if you don't tolerate oral magnesium well.


  • Sleep is a vital part of your day. Address any sleep problems you have, making sure you are following good sleep hygiene, and supplementing if necessary to insure a good 7-9 hours of sleep nightly. 
  • Exercise: Discover forms of exercise you love - and do these activities regularly. Brisk walking is sufficient for most people. For even greater benefits, consider adding strength and interval training to a program of daily walking. Use common sense to avoid overly stressful exercise, and incorporate rest days to reap the full benefit of your exercise workouts. 
  • Treat stress naturally: Sustained stress can raise internal cortisol levels which can disrupt immune balance.  Look for relief in exercise, meditation, hobbies, or counseling.  

Integrative treatment

Low dose naltrexone. In addition to a nutritional and lifestyle approach, there is one medication available through compounding pharmacies that has shown some promise in modulating autoimmune disease. Naltrexone – a medication that in conventional doses is used to reverse narcotic effects – can be compounded into small doses. Taking 1.5-4.5 mg at bedtime blocks opiate receptors in the middle of the night (causing transient dream disturbance in some), and as the body re-sets those receptors it also seems to exert a balancing effect on the imbalanced arms (brake pedal/gas pedal) of the immune system. Naltrexone requires a physician’s prescription.

Methylation. You might remember from high school chemistry a "methyl" group, one carbon atom and three hydrogen atoms. Our body exchanges methyl groups to perform almost every vital action of generating energy, detoxifying harmful substances, and balancing our immune system. Working with a knowledgeable physician and your own genetic information, you can identify where in the methylation chain your own physiology needs extra support. Methylated B vitamins, appropriately dosed, can reduce autoimmune symptoms and increase general energy.

Nutritional evaluation. Despite anyone's best efforts to consume an excellent balance of vital nutrients, the question remains: what have you absorbed and what do you still need? A full nutritional evaluation, such as the one provided by Genova Diagnostics NutrEval panel, can reveal some surprising opportunities for intervention and possible improvement of your overall health, as well as specific symptoms. Following up with a good look at your digestive system (I use Genova's GI Effects Panel), can identify some of the reasons you might not be absorbing all your nutrients.


General measures of good health should also reduce your risks of getting autoimmune disease.

  • Avoid unnecessary antibiotics. Everyone should hold strong reservations about taking antibiotics or consuming meat laced with probiotics or meat from animals nourished on grains. When a course of antibiotics is required, the intestinal flora takes months or years to recover without assistance, if it ever recovers. If one of my patients must take antibiotics, I recommend a vigorous re-introduction of pre- and probiotics, through food and supplements, with good diversity. It is not uncommon for a new patient to report, "I don't take antibiotics much, maybe just once or twice a year." My well-established patients go decades without needing them. Homeopathic treatment and general immune vitality help people recover from most infections without antibiotics. Even public health departments are on the bandwagon for avoiding unnecessary antibiotics.
  • Watch for food sensitivities. I think it is reasonable for anyone to take a trial 4-6 weeks off of grains, legumes, and dairy, if for nothing more than an increased awareness of how pervasively those foods appear in our often unconsciously made food choices. I tolerate cheese and some other dairy, but was shocked to find during a month off dairy, that I was chatting away, pulling the cheese out of my Caesar salad and chewing my cheese-burger without thinking! If you find yourself with any kind of sensitivity to a food (rashes, gastrointestinal distress, headaches), I would recommend avoiding that food and addressing your gastrointestinal health fully before reintroduction.
  • Gastrointestinal health is key. Some day in the future, physicians will take a stool sample for analysis, and provide you with an encapsulated dose of whatever your intestines are lacking. In the meantime, consider any GI symptom, even if it just seems mildly annoying, as evidence of an imbalance and a call to action. 

From Dr. Deborah's Desk

The most common autoimmune diseases in my practice are actually Hashimoto's thyroiditis and multiple sclerosis. I can think of one example of each who walked in the door – years ago before I made the connection myself – and told me that they were gluten-sensitive and could keep the best handle on their health problems by strict gluten avoidance. Continuing dietary modifications have kept them both in fairly stable health, and completely lacking in any wishful thinking about gluten! 


This information is provided for educational purposes only, and any individual diagnosis or treatment should be determined by you and your doctor. See Additional Information.

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