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Autoimmunity – why your doctor is missing the point


Autoimmune diseases are characterized by the body’s immune responses being directed against its own tissues, causing prolonged inflammation and subsequent tissue destruction. Conventional practitioners may insist on their belief that autoimmune diseases are “idiopathic”, which means ‘of unknown origin’, and apply their conventional treatment aimed at “managing” the disease with immunosuppressing drugs – corticosteroids. The idea is to “suppress” the immune response.

However, recent abundant scientific studies have largely demonstrated that autoimmune diseases are caused and perpetuated by genetic predisposition, environmental factors, and immune regulation – not immune suppression – which means that the corticosteroids are not the solution at all as they’re not addressing the root of the problem.

In functional medicine we go to the root-causes before thinking of applying treatments or fixating on diagnosis.

Let’s see these three underlying root-causes of autoimmunity one by one:

Environmental factors causing autoimmunity

Current data suggests that environmental factors, such as infections, gut microbiota, toxic chemicals, and dietary components have up to a 70% contribution to loss of immune tolerance. Let’s see these in detail:


An autoimmune disease may be induced or triggered by infectious agents including viruses, bacteria, and fungi.

Viral Infections

Many viral infections have been implicated in the development of auto-immune disorders, like for example Epstein-Barr Virus (EBV) in rheumatoid arthritis (RA); mumps in thyroid disease; or HA (Hepatitis A) in type I diabetes.

Gut Microbiota

There is growing evidence that the commensal bacteria in the gastrointestinal tract (the gut microbiota) influence the development of autoimmunity. An abnormal ratio of pathogenic bacteria or yeast will lead to dysbiosis, inflammation, leaky gut syndrome, and auto-immunity.

Bacterial Infections

Many bacteria have been implicated in the etiology of autoimmunity, such as Yersinia enterocolitica, Chlamydia, Borrelia burgdorferi, Klebsiella pneumonieae, or Shigella flexneri in Rheumatoid Arthritis; or E. coli in Primary Biliary Cirrhosis (PBC). Chlamydia often precedes the initiation of autoimmune diseases. Recent studies demonstrate a link between mycoplasmal infections and RA. A study published in 2000 showed that 38.5% of patients diagnosed with MS (Multiple Sclerosis) had a positive serologic reaction to Borrelia. EBV and CMV (cytomegalovirus) have been linked to the development of MS and lupus.

It is essential to note, however, that in many cases, it is not a single infection but rather the “burden of infections” from childhood that is responsible for the induction of autoimmunity.


An early report on the presence of an immunological response to Candida albicans in the synovial fluid and peripheral blood lymphocytes suggests that even fungi may induce autoimmune disease.

Environmental Toxins

For example, occupational exposure to crystalline silica has been linked to RA, systemic sclerosis (SSc), SLE and anti-neutrophil cytoplasmic antibody (ANCA)-related diseases. Solvents, or chemicals with similar structures, including vinyl chloride, epoxy resin, trichloroethylene (TCE), perchloroethylene, or mixed solvents were confidently associated with SSc. Other studies supported a likely association between solvent exposure and MS. There is some evidence for an association of cosmetics with Systemic Lupus Erythematosus (SLE ), RA and primary biliary cirrhosis (PBC). Smoking can cause PBC, Chronic Obstructive Pulmonary Disease (COPD), RA, autoimmune thyroiditis. Collagen implants can cause SLE, Sjorgren’s, SSC. Vaccinations – can cause polyarthritis nodosa, SLE, RA, Myasthenia Gravis (MG), and more. Heavy metals are also well known for their immunosuppressive effects that impair the immune system’s response to infections. Arsenic concentration in the urine has been associated with Type II diabetes. Cadmium also. Mercury toxicity –including mercury amalgams- can cause autoimmune thyroiditis.


Numerous studies have demonstrated the positive link between organochlorine pesticides with the development of rheumatoid arthritis, systemic lupus erythematosus, hypothyroidism, Parkinson’s disease, and more.

Pharmaceutical Drugs

  • Allopurinol (medicine to treat gout) – can cause immune haemolytic anaemia
  • Captopril (a hypertension drug) – can cause autoimmune thrombocytopenia
  • Cholopromazine (antipsychotic medication) – can cause anti-phospholipid syndrome, haemolytic anaemia
  • Oestrogens (from equine source) – can cause SLE, PBC, RA
  • Penicillin (antibiotic medication) – can cause autoimmune liver disease and haemolytic anaemia
  • Rifampicin (antibiotic medication)– can cause autoimmune thyroid

Dietary Factors

The constant introduction of competitive new food experiences that come from new food products, new breeds of food plants and food animals, genetic modifications, chemical ingredients, flavours, and preservatives, a significant increase in the incidence of autoimmune diseases has been observed over recent decades. The most detrimental dietary factors leading to autoimmunity are gluten, low levels of vitamin D, lactose intolerance, and xenobiotics of the food industry, like food additives and pesticides. Advanced glycation end products or AGEs – toxins formed in foods processed or cooked at high temperatures, especially BBQ meats, but also in grilling, broiling, roasting, searing, and frying – also lead to autoimmunity.

How can we help people suffering from autoimmunity with functional medicine

The correct treatment of autoimmune disorders requires proper laboratory investigations to pin-point and determine both extrinsic causative factors (drugs, chemicals, microbes, and other environmental/xenobiotics) and intrinsic causative factors (inflammation, digestive insufficiency, dysbiosis, etc.) that can induce or promote the development of autoimmunity. Once the findings are there, we can proceed to remove these offenders with researched based detoxification protocols, epigenetics, diet, and lifestyle. In terms of detoxification of heavy metal, plastics, pesticides and other chemicals, we can use soft oral chelators like cilantro extract, humic acid, MSM, DMSA, glutathione, sulphoraphane, Ca-d-glucarate and specific minerals to avoid nutrient depletion during chelation

We can also look at putting you on a gluten and dairy free diet without needing to test for these two food intolerances as gluten is involved in the pathogenesis of autoimmunity, and dairy mimics it. To fix the gut we need to rebuild normal pH with diluted chloric acid & pepsin; rebuild digestion; and rebuild immune barrier sIgA with botanicals, colostrum, amino-acids, and vitamin D, among others.

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