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Treating autoimmune conditions with functional medicine

Treating autoimmune conditions with functional medicine
March 18 , 2021
Nour Al Nahlawy Nour Al Nahlawy
A pharmacist, a health coach and a mom, graduated from The Faculty of Pharmacy from Ain Shams University, Egypt.  She studied holistic... more

If you have recently been diagnosed with an autoimmune condition like rheumatoid arthritis, lupus, Hashimoto’s thyroiditis, multiple sclerosis, or Crohn’s disease, you must be frustrated. It’s not easy when the doctors tell you that your body is attacking itself. However, from the functional medicine perspective, there is always hope.

Your immune system was designed to fight foreign substances or foreign organisms. It was designed to protect you. It does this by creating an inflammatory response: summoning white blood cells to fight the foreign organisms and calling on clotting factors to stop bleeding.

However, when the immune system is constantly in an inflammatory response, you can see why this could be a problem. If your immune system is constantly fighting an organism, stress, or food sensitivities, it might become dysregulated. It could start attacking your own tissue.

Disease begins in the gut

I believe Hippocrates' saying: "All disease begins in the gut." Modern medicine has proved this quote to be correct. 70% of our immune system is in our gut. We also carry billions of friendly bacteria in our gut that helps crowd out the harmful bacteria and assist our immune system. Science is constantly discovering new functions for this friendly bacteria.

Frequent use of antibiotics and eating animal foods that were fed antibiotics will kill those friendly bacteria. Working with your doctor to treat any infection is crucial.

After that, start nourishing the friendly bacteria by eating prebiotics - foods that nourish the gut bacteria, eat fermented foods containing healthy bacteria, and/or take a probiotic supplement.

Sometimes prebiotics can hurt your gut if you have inflammatory bowel disease. Please work with your health provider to select the best food/supplement for you.

Generally, a probiotic that contains a variety of bacteria is better than one that contains one strain with billions of numbers. We need the variety. Saccharomyces boulardii is a strain that should be included in a probiotic for an autoimmune patient, provided that they have no yeast sensitivity.

Check for food sensitivities

The leaky gut syndrome is a problem that is very common in people with autoimmune conditions (1). In this syndrome, the intestinal cells are separated from each other, and the food starts to leak into the blood, creating an immune response.

Everyone is different when it comes to food sensitivities. A test called the IgG food sensitivity test is used to identify some of the foods your immune system is attacking... However, no test is 100% accurate, and sometimes an elimination diet with a qualified practitioner can be the best way to identify food sensitivities.

Some common food sensitivities include gluten, eggs, fish, dairy products, yeast, soy, and corn. However, you can be sensitive to anything when it comes to leaky gut.

Continuing to eat these foods will keep your body in a state of inflammation. This prevents your immune system from healing. The confusion state goes on.

Eliminating the food you are sensitive to is only the first step. After that, you need to start healing the leaky gut.

Correcting Vitamin D, A, and zinc deficiencies

Vitamin D has gained huge popularity for its benefits for the immune system. A good level of vitamin D is 40-60 ng/ml for most people. When the levels are higher or lower, it could negatively affect the immune system.

Sunlight is the best way to get vitamin D. 10 minutes a day is enough, provided that a large area of your skin is exposed and you're not wearing any sunblock.

If your levels are very low, it's important to supplement with vitamin D gradually. Start with 2000 IU and talk to your doctor about the dose you need and the duration.

I do not recommend the 50,000 IU dose weekly because it might increase the calcium levels in your blood, leading to calcification of soft tissues, including your arteries, a common cause of narrowing of the arteries and heart disease.

Vitamin D uses magnesium. It's important to make sure your magnesium levels are sufficient when using a vitamin D supplement. If you are susceptible to high calcium levels, you might want to consider vitamin K2 as well. This vitamin specifically directs calcium towards the bones and away from soft tissues.

Retest vitamin D after 2 months and make sure that the levels do not exceed 60 ng/ml, especially if you're suffering from an autoimmune condition.

Vitamin A is less-known for its effect on the immune system than vitamin D, but it's actually crucial for a well-regulated immune system.

Vitamins A and D actually have a lot in common. They both can activate the same receptors, which means that if you ramp up vitamin D levels too quickly, vitamin A's effect on the cells could decrease. They are both steroid hormones, and they are both fat-soluble vitamins. A good balance of both is crucial.

Vitamin A is found in foods in two forms: beta-carotene, which must be converted in the body to active vitamin A, and active vitamin A or retinol. Some people can not effectively convert beta carotenes found in plants to active vitamin A.

Active vitamin A is only found in animal foods like egg yolks, butter, beef, and fatty fish like mackerel. Checking your vitamin A levels and correcting any deficiency with your doctor is essential for helping your autoimmune condition.

Zinc is involved in more than 300 enzymes and cellular reactions in the body. It is a crucial element for immune system regulation. "Regulation" is the keyword here. A regulated immune system can differentiate between your cells and foreign invaders.

A meta-analysis in 2018 described the role of zinc-deficiency in several autoimmune conditions like lupus, rheumatoid arthritis, Hashimoto's, and diabetes type 1. This relationship has been discovered since the 70s.

Checking the zinc levels in the serum is not very accurate because it's affected by what you ate the day before. A better way to check minerals in the blood is to check their levels inside the red blood cells (RBC zinc). This ensures that the levels represent a longer-term level because the red blood cells live for around 4 months.

Manage stress levels

Stress creates a fight/flight response in your body. When this happens, your body prioritizes survival activities and puts everything else on hold. This includes your digestion, your elimination, and detoxification processes, and guess what? Your immune system!

Your body's wisdom does not think it's the right time to fight something else when you need to run for your life. When you're in a constant state of stress, this will wreak havoc on the immune system, and it will further become dysregulated.

It's important to note that stress does not need to be a traumatic experience to have this effect on your body. Just running around all day from task to task will trick your body into these dynamics. Your body cannot differentiate between running away from a tiger or doing errands all day without rest, exercising vigorously, or even constantly fighting with your teenagers!

If you're not aware, any of these activities can have the same effect on your organs. Try taking breaks to breathe deeply every twenty minutes. Yoga, meditation, and other mind-body activities have helped thousands of people get out of this continuous stress response. Journaling is also an effective stress-managing activity.

Before saying this is not for me, you’ve got to try everything for at least 2-3 weeks to experiment its effect until you find what resonates with you and what you can sustain.

These were only a few ways used by functional medicine to approach autoimmune conditions. Identifying toxins in the body and getting rid of them is another tool used to reverse an autoimmune condition.

In functional medicine, we don't like to label a patient with a disease: a Hashimoto's patient or an MS patient. Instead, we treat each patient separately and consider all aspects of his life that lead him/her to reach this state.

Emotional and spiritual health is just as important as physical health. In fact, it is usually the emotional side of a person's life that triggers an autoimmune condition.



  1. Fasano A. Leaky gut and autoimmune diseases. Clin Rev Allergy Immunol. 2012 Feb;42(1):71-8. doi: 10.1007/s12016-011-8291-x. PMID: 22109896.
  2. Yang CY, Leung PS, Adamopoulos IE, Gershwin ME. The implication of vitamin D and autoimmunity: a comprehensive review. Clin Rev Allergy Immunol. 2013;45(2):217-226. doi:10.1007/s12016-013-8361-3
  3. Sanna A, Firinu D, Zavattari P, Valera P. Zinc Status and Autoimmunity: A Systematic Review and Meta-Analysis. Nutrients. 2018;10(1):68. Published 2018 Jan 11. doi:10.3390/nu10010068


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