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Research Suggests an Imbalanced Gut Microbiome May Cause This Debilitating Autoimmune Disease

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Research Suggests an Imbalanced Gut Microbiome May Cause This Debilitating Autoimmune Disease

Multiple sclerosis, MS, is a chronic autoimmune condition that affects around 2.5 million people worldwide and is more common in people whose biological sex is female.

While MS can occur at any age, it is most often diagnosed between the ages of 20 and 40. It is most common in countries with temperate climates, including the northern United States, Canada, New Zealand, southeastern Australia, and Europe. In contrast, parts of Asia, Africa, and America that lie on the equator have significantly lower levels of MS.

A functional medicine approach to Multiple Sclerosis focuses on diagnosing the root cause to uncover infectious, nutritional, and environmental factors triggering the immune attack and imbalances that interfere with healing and regeneration.


What Is Multiple Sclerosis

Multiple sclerosis involves imbalances in immune and mitochondrial function that lead to the demyelination of nerves. Nerves allow the body to send signals to provide a communication network for the brain to send signals to the rest of the body.

In multiple sclerosis, the immune system mistakenly attacks the protective coating surrounding the nerves (myelin) in the brain and spinal cord, impairing the body’s method of signaling and communication.

The immune system-mediated attack on the nerves that occurs with MS causes damage that interrupts the transmission of nerve signals between the central nervous system and the rest of the body. When the myelin coating of nerves is damaged, the body begins to lose control over movement and muscle function, vision, balance, and the ability to feel various sensations.

In addition to nerve damage and dysfunction, abnormalities in mitochondrial energy production also contribute to nerve dysfunction and MS symptoms. Mitochondria are organelles that are responsible for producing energy that fuels cells and contributes to cell signaling.

Multiple Sclerosis Signs & Symptoms

Multiple sclerosis causes a variety of symptoms that can differ between patients.

There are four main types of MS:

  • Relapsing-remitting
  • Secondary-progressive
  • Primary-progressive
  • Progressive-relapsing

The most common form of MS is relapsing-remitting, the mildest form, which occurs in about 85% of individuals. This results in occasional flare-ups in symptoms known as “relapses,” with relatively symptom-free periods in between. The course of the other forms of MS is rarely predictable and leads to slowly worsening symptoms with or without flare-ups.

During relapses, some common symptoms occur due to damage to the myelin sheath and nerve dysfunction, which include:

  • Vision problems
  • Numbness and tingling
  • Fatigue
  • Electric-shock sensations when bending the neck forward (Lhermitte sign)
  • Muscle problems, such as spasms, weakness, and stiffness
  • Difficulty thinking and brain fog
  • Pain
  • Bladder and bowel problems
  • Challenges with speech and swallowing

One of the earliest symptoms noticed by individuals with multiple sclerosis is blurred vision or eye pain due to damage to the optic nerves. Other common symptoms include numbness and tingling in the arms, legs, or face.

What Causes Multiple Sclerosis

Multiple sclerosis is caused by various interacting factors that trigger an immune response in susceptible individuals. Autoimmune diseases like multiple sclerosis occur when the body’s normal immune defenses go awry and attack the body itself instead of pathogens or foreign substances. Various environmental, infectious, and nutritional factors trigger an autoimmune attack on the nervous system in genetically susceptible individuals.

Imbalanced Gut Microbiome

Recent research suggests that gut health plays an essential role in the development of MS. For example, when the gut is damaged and becomes leaky, it can allow small particles of food or pathogens to cross into the body, triggering inflammation and immune response. Substances like gluten, casein (a protein found in milk), bacteria, viruses, medications, and stress can damage the gut lining, allowing toxins, microbes, and undigested food particles to enter the bloodstream directly.

In the blood, immune cells may recognize these substances as similar to the body’s proteins and get confused. This may lead to an immune attack on tissues like myelin that causes destruction in a process known as molecular mimicry.

A leaky gut can also cause decreased absorption of certain essential vitamins and minerals such as vitamin D, essential fatty acids, and B vitamins.

Nutritional Factors

The brain needs B vitamins, especially B1 (thiamine), B9 (folate) and B12 (cobalamin), omega-3 fatty acids, and iodine to make the myelin that protects nerves. Low levels of these nutrients may correlate with a greater risk of multiple sclerosis. An imbalanced gut microbiome can lead to these nutrient deficiencies.

Environmental exposures

Environmental exposures contribute to autoimmunity, inflammation, and damage to nerves. When metals and chemicals like mercury, copper, cadmium, lead, and iron accumulate in the body, they can damage cells and contribute to inflammation. When cells become damaged, the immune system may mistake them for foreign invaders and begin to attack its own tissues, triggering an autoimmune process.

Evidence shows that smoking and exposure to second-hand smoke also increase the risk of developing multiple sclerosis and relapses.

MS occurs more frequently in areas that are farther from the equator. People living further from the equator are exposed to lower sunlight year-round. Therefore, they tend to have lower levels of naturally-produced vitamin D, which is thought to support immune function and protect against immune-mediated diseases like MS. Small increases in environmental and body temperature can temporarily worsen signs and symptoms of MS.


Exposure to various bacteria, viruses, and molds and the toxins they can produce can also trigger an autoimmune attack on the body in genetically-susceptible individuals.

Patients with MS commonly have higher levels of bacteria, including Mycoplasma pneumonia, Chlamydia pneumonia, and Clostridium perfringens, in their bodies.

For example, MS patients may have colonization of Clostridium perfringens bacteria in the gut which can produce the toxin epsilon, which is associated with nerve damage that occurs in MS.

Similarly, although most people infected with these common viruses do not develop multiple sclerosis, Epstein-Barr virus (EBV) (the virus that causes infectious mononucleosis) and human herpesvirus 6 are associated with multiple sclerosis and relapses of the disease.


While MS is not directly inherited, genetic factors can contribute to risk. Those with a family history of MS or other autoimmune conditions have an increased risk. The most significant genetic risk factor is an allele from the MHC class II HLA-DRB1 gene (HLA-DRB1*15:01), which increases MS risk threefold.


Methylenetetrahydrofolate reductase (MTHFR) is a key folate metabolizing enzyme that occurs in different versions in different people. Methylation adds methyl groups to DNA to alter its activity. Two common genetic alterations, C677T and A1298C, are associated with decreased activity of this enzyme which can impair detoxification and lead to increased levels of plasma homocysteine that can damage nerves and increase susceptibility to MS.

How is Multiple Sclerosis Diagnosed

Multiple sclerosis is diagnosed by a comprehensive assessment, including a physical exam, imaging, and laboratory studies. Comprehensive neurological and eye exams can detect the results of decreased nerve function. An MRI is frequently used as a non-invasive method to detect damaged myelin in the brain and spinal cord.

Another diagnostic study that may be used to evaluate multiple sclerosis is an evoked potential test where electrodes are placed on the head and various body parts to measure chemical responses and determine if nerve transmission is delayed in different areas.

A spinal tap where a needle is used to remove a fluid sample from surrounding the spinal cord can also help confirm multiple sclerosis and rule out other diseases that might mimic MS.

Biomarkers of MS are under investigation that may lead to blood test detection for the disease in the future.

Diagnosing the Root Cause of Multiple Sclerosis

Functional medicine laboratory tests can help delineate the root causes of the inflammation and immune dysregulation that occur in multiple sclerosis. By assessing these markers and knowing exactly where to focus, practitioners can help slow the progression of the disease, reduce the frequency and severity of relapses, and minimize the impact of symptoms.

Markers of Autoimmunity and Infections

The Neural Zoomer Plus test measures common autoantibodies associated with neurological autoimmunity, including demyelination antigens like anti-tubulin, anti-myelin basic protein, anti-myelin oligodendrocyte glycoprotein, and anti-myelin proteolipid protein that can indicate nerve damage in MS. It also detects antibodies against infections that can have neurological impacts such as herpes viruses and EBV.

Gut Health

The GI-MAP assesses relative amounts of healthy and unbalanced gut bacteria, inflammation, and leaky gut markers, helping uncover imbalances that can trigger autoimmunity and perpetuate the cycle of inflammation.

Food sensitivities can also contribute to increased intestinal permeability, inflammation, and autoimmunity. Foods to which an individual is sensitive to can be identified through various tests, including blood spot or blood draw for both food sensitivity and food allergens.

Heavy Metals

A heavy metals profile measures any heavy metals that have accumulated in the body and may be contributing to nerve damage and immune dysfunction.

Vitamins and Nutritional Status

Deficiencies in Vitamin A, B vitamins, vitamin D3, and omega-3 fatty acids are associated with a higher risk of MS and worsening nerve function. The functional status of nutrients within the cell can be assessed with a micronutrient panel to uncover and target any deficiencies.

Methylation Status

Balanced methylation is required for detoxifying toxins like mercury and heavy metals that can damage nerves. Different variations of MTHFR genes seem to be associated with the risk of MS and impact detoxification function in the body.

Conventional Medical Treatment for Multiple Sclerosis

Conventional medications are often used to target symptoms to slow the progression of MS, minimize the frequency and severity of relapses, and treat specific symptoms. These drugs target the symptoms of MS but do not address the root cause.

For example, to reduce the impact of MS relapses, corticosteroids are used to reduce nerve inflammation, while plasmapheresis is also used to slow the immune attack. This involves removing the liquid portion of part of the blood (plasma) and separating it from the rest of the blood cells, which are then mixed with a protein solution (albumin) and put back into the body.

Several disease-modifying therapies are used depending on the type of MS to modify the progression of the disease. The drug beta-Interferon and the monoclonal antibody natalizumab (Tysabri) are believed to block the blood-brain barrier to prevent T cells of the immune system from accessing the central nervous system and wrongly attacking myelin and nerves. While it can help slow disease progression, interferon can cause side effects like flu-like symptoms, allergic reactions, depression, anemia, heart problems, and liver damage. Another conventional medication used in multiple sclerosis is glatiramer acetate (Copaxone, Glatopa). This drug is similar to myelin proteins, which is thought to help protect myelin from damaging autoimmune attacks.

Treating the Root Cause of Multiple Sclerosis


A gluten-free, individualized anti-inflammatory diet can help reduce inflammation and autoimmunity in patients with MS. Various diets have been used in patients with multiple sclerosis, including The Wahls Protocol, which is a modified Paleo diet high in vegetables, grass-fed meat, and wild fish, and largely free of grains including gluten, dairy, and starches and augmented with targeted nutraceuticals to improve mitochondrial function and promote the production of myelin.

Since diet plays an essential role in shaping the bacteria in the gut, a dietary approach that heals the gut and balances the microbiome can help to modulate immune responses and reduce inflammation. A diet rich in unprocessed whole foods that incorporates probiotic-rich foods like miso, kimchi, and sauerkraut combined with prebiotic-rich foods like leeks, artichokes, garlic, and beans that nourish healthy bacteria is critical for repairing the intestinal lining and reducing inflammation. A high vegetable diet that provides natural fiber and phytonutrients improves inflammation and reduces relapses of MS.

Herbs & Supplements

If deficiencies are uncovered, supplements like vitamin D, omega-3 fish oils, Ginkgo Biloba, and glutathione can help restore balance and influence the immune system.

  • Vitamin D has been shown to help regulate the immune system, with lower levels of vitamin D associated with a greater risk of multiple sclerosis.
  • Omega 3 fish oils are effective at regulating inflammation in the entire body and helping to heal the gut. Research suggests that those who supplemented their low-fat diet with omega-3 fatty acids positively affected the quality of life in patients with relapsing-remitting MS.
  • Ginkgo Biloba shows promise for improving some aspects of cognitive function in MS.
  • Glutathione is a powerful antioxidant in the body that supports detoxification and can help reduce inflammation. Oxidative stress contributes to mitochondrial dysfunction and inflammation that worsen nerve damage in MS.

Due to the potential for immune stimulation, MS patients should work with their practitioner to determine if they should avoid immune-stimulating supplements like echinacea, oral garlic supplements, zinc, astragalus, cat’s claw, maitake mushroom, mistletoe, stinging nettle, and some antioxidant vitamins.

If viral infections are detected, monolaurin from coconut oil may help treatment for Herpes Simplex Virus, HSV, and EBV. At the same time, lysine supplements and lysine-rich foods like spirulina are effective at treating HSV infections.

Lifestyle Changes

Physical therapy and individualized mindful movements such as yoga and tai chi can be helpful for individuals with MS and may help with fatigue, strength, muscle tone, balance, and coordination.

Stopping smoking and avoiding exposure to second-hand smoke help slow the progression of disability. Similarly, avoidance of excessive alcohol may help prevent MS relapses.

Since the symptoms of multiple sclerosis can worsen with elevated body temperature, some people find it helpful to avoid exposure to heat and use cooling devices like vests or scarves.

Integrative Medicine (IM)

Integrative medicine combines treatments from conventional medicine and Complementary Medicine for which there is some high-quality evidence of safety and effectiveness. Research suggests that meditation, reflexology, massage therapy, yoga, diet, acupuncture, reiki, and Tai Chi can improve fatigue, quality of life, and pain.


Multiple sclerosis is a potentially disabling disease of the central nervous system, including the brain, spinal cord, and optic nerves. A dysregulated immune response attacks the protective covering of nerves (myelin) which causes problems with communication between the brain and the rest of the body.

Signs and symptoms of MS vary between individuals, with common symptoms including numbness, weakness, unsteady gait, and vision problems. Multiple sclerosis is diagnosed by a comprehensive assessment, including a physical exam, imaging, and laboratory studies. Functional medicine laboratory tests can help delineate the root causes of the inflammation and immune dysregulation that occur in multiple sclerosis.

Treatments for multiple sclerosis aim to slow the progression of the disease, reduce the frequency and severity of relapses, and minimize the impact of symptoms. An individualized anti-inflammatory diet and targeted supplements can help reduce inflammation and autoimmunity in patients with MS. Lifestyle approaches like mindful movement, meditation, and avoiding smoking and alcohol can improve quality of life.

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