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Managing an Autoimmune condition may require implementing lifestyle changes that are adapted to an individuals specific autoimmune triggers.  One diet, supplement or lifestyle change will not cause remission and often trial and error of various strategies is required to work out what has the biggest impact for your Autoimmune expression.  Most important is forming a routine involving such changes as this will ensure adherence.  

Some strategies involved in Autoimmune management may involve; identifying and reducing triggers, balancing the ratio of TRegs and TH17 cells, improving immune intolerance and improving immune barriers using diet, nutraceuticals and lifestyle strategies.  Lab testing and accurate history taking is essential to understanding which strategies to implement.

Where to start?

The simplest way to start addressing an Autoimmune condition is to identify and address your personal triggers.  The following may need to be considered: stress, sleep, exercise, reducing toxic load, microbiome diversity, addressing food sensitivities, balancing the microbiome and healing the gut immune barrier.

managing autoimmunity


Data suggests that sleep disorders are correlated to a higher risk for Autoimmune diseases.  Circadian cycle proteins and hormones have a direct effect on the immune system, inflammation and Autoimmune diseases through a possible dampened immune response against pathogens and most certainly a breakdown of immunologic self-tolerance.   Interestingly, studies show that sleep deprivation results in elevation of several proinflammatory cytokines, including IL-1, IL-1β, IL-6, IL-17, and TNF-α.  (IL-17 remained elevated for 7 days following sleep deprivation,  indicating the pivotal role IL-17 played in coordinating the inflammation).  Furthermore, In a murine model of Lupus, sleep deprivation was shown to contribute to an earlier onset of the disease. The association between sleep disorders and neurological Autoimmunity has also gained much interest in research recently.

The Immune system modulates and primes its cells when we are asleep.  Its important to feel rested when we wake up.  Unhealthy sleeping habits, eg looking at your phone until late at night are habits that may need to be addressed.  Consistency of when you fall asleep and wake up is important.   Cortisol levels should be high in the morning to facilitate waking and getting started and then come down as you progress through the day.  Whereas Melatonin levels are low in the morning and increase as we approach bedtime, instigating sleep.  Melatonin increases immune cytokine production whereas Cortisol decreases it.  Interestingly those with autoimmune flare ups have disruptions in these circadian rhythms.  There is profound impact in Autoimmune expression when someone gets continuous sleep.  Some observations that may be worth noting:

Do you feel you have continuous sleep every night?

Do you have a hard time falling asleep or staying asleep?

Do you have a regular schedule for bedtime and awakening?


We need stress to stay healthy, positive and to provide us with purpose. Stress at a manageable level can have an anti-inflammatory affect i.e. at biochemical cellular level cortisol can inhibit NFKB inflammatory pathways.  However prolonged stress can activate proinflammatory cytokines IL6 and TH17 cells and trigger Autoimmunity, this has been validated in studies. 

It is important to consider ways to adapt to stress so that it does not get out of control i.e. to understand your personal stress reduction options as uncontrolled stress can trigger Autoimmunity.  Many studies have explored which factors help reduce stress.  Different things will work for different people for example some people may find meditating stressful!  Unhealthy relationships that lead to stress may be a factor worth considering i.e. work relationships and family/partner relationships.   Healthy relationships trigger the release of natural opioids which can upregulate Treg cells as per studies. 

It is very important to realistically assess your level of stress (both physical stressors and mental stressors) and the impact it may be having in other areas of your life such as sleep, eating, relationships as prolonged uncontrolled stress over time will have a profound impact at biochemical and cellular level particularly for the immune system.


A sedentary lifestyle is a BIG problem with Autoimmune patients.  There have been many studies on the effect of exercise on the immune system and Autoimmunity and it has shown to have a profound impact.  For example a recent study shows that a supervised, well-regulated and controlled exercise regimen alleviates CNS lupus and could potentially serve as an intervention strategy to improve the quality of life.  Also studies suggest a disease-specific beneficial effect of exercise on Regulatory T cells and improved immune tolerance. 

Autoimmune patients have an underlying inflammatory response and constant depletion of antioxidants.  Therefore it is important to get the right balance of exercise and recovery time since over-training can promote IL6 inflammatory cytokines which can have a negative effect.  The higher the exercise intensity the more inflammation and free radicals produced. 

Light intensity - heart rate 40-55% of max heart rate, does not induce sweating eg a brisk walk.

Medium Intensity - 55-69% of max heart rate, with sweating after 10 mins, breathing is deeper. 

High Intensity - 70% or greater max heart rate, will sweat after 3-5 mins, breathing is deep and rapid

The benefits of exercise intensity varies between people and you will need to see what works for you.  High intensity exercise releases growth hormone, opioids, nitric oxide, brain derived neurotrophic factor and improves immune system and Insulin sensitivity.  However it does increase oxidative stress and the risk of overtraining syndrome and inflammation.   

It's important for Autoimmune patients not to over train to recover from exercise so it doesn't become inflammatory and it recovers.  Autoimmune patients must work out what works best for them in respect to:

Frequency of workouts

Duration of workouts

Recovery time needed from workouts

Intensity of workouts



Our bodies must detoxify chemicals to remove them from the body.  Hepatic biotransformation is the process by which substances that enter the body are changed from hydrophobic to hydrophilic molecules to facilitate elimination from the body i.e. the biotransformation process in the liver transfers fat soluble compounds to water soluble so that they can be eliminated from urine, sweat etc.  If chemicals are not removed by biotransformation then they need to be removed by antioxidants to prevent damage to body tissues.  Glutathione is involved in the liver biotransformation process and also in neutralising free radicals. 

The liver biotransformation pathways are called sulphation, methylation, glucuronidation etc and need various nutrients cofactors to support their clearance of chemicals.  Our genes give us uniqueness in liver pathways i.e. some people don't clear plastics or medications very well.  Therefore various elements of diet or lifestyle in an individual determine how these genes express.  Optimising biotransformation phase 1 and 2  pathways with nutraceuticals can help with Autoimmunity.  Heavy metals and toxic poisons can't be bio-transformed by your liver whereas pesticides, solvents, plastics, medications and air pollutants can be. Those chemicals that can't be cleared create oxidative stress, deplete glutathione, loss of tolerance and Autoimmunity.  


Aflatoxins - Stored grains, dairy products, vegetable oils, cosmetics

Formaldehydes - Adhesives, foams, fabric finishers, drinking water, shaving cream

Trimellitic and Phthalic Anhydride - PVC pipes, fibreglass plastics, protective coating resins, tanning agents, perfumes, insect repellents.

Isocyanates - Upholstery and mattress foams, window and wall insulation, carpet underlay, adhesives, footwear pads

Benzene - Cigarette smoke, petrol fumes, traffic exhaust, pesticides, glue

BPA - Plastic water bottles and containers, coating of beverage cans, sales receipts

Tetrabromobisphenol A - Electronics, soil contamination, vegetable and plant contamination

Tetrachloroethylene - dry cleaning chemicals, degreaser solutions, clothes spot removers

Parabens - cosmetics, shampoos, shower gels, skin moisturisers, food additives


  • Water Filters - House, drinking water, shower head

  • Steel, Glass, Ceramic, cups and food containers and plates (no plastic!)

  • Chemical free cleaning products - soaps, Dishwasher tablets, Clothes detergent

  • Natural Copmound insecticides

  • Fire retardant-free upholstered furniture, mattresses

  • Chemical free cosmetics, shampoos, moisturisers

  • Flooring - Limit carpets and vinyl and use wood flooring or stone

  • Air Filters - use HEPA filter


Amino Acids, Micronutrients, Medium Chain triglycerides (eg coconut oil), Quercetin, Milk Thistle Extract, Dandelion Extract, Panax Ginseng, Molybdenum and Antioxidants.


  • To improve antioxidant status

  • To clear haptens

  • To support liver detoxification phase 1 and 2 pathways

  • Support glutathione recycling - Cordecps, Alpha -lipoic acid, L-glutamine, Selenium, N-acetyl Cysteine


  • Strategies to support sweat, lymphatic drainage and bowel movements

  • Exercise encourages elimination of compounds​



The association between bacteria and Autoimmune disease is well researched; alteration of microbiome ‘dysbiosis’ can induce Autoimmune disease in people with certain genetic backgrounds and environmental factors.  Diversity in the microbiome is key for promoting Immune Tolerance and protecting against Autoimmunity.  It is important to eat a broad list of different plant fibres in your diet.  All the different bacteria in the microbiome have enzymes involved in different metabolic functions.  Eating the same foods every day can be detrimental to improving and maintaining a healthy microbiome.   

FOODS TO ADD - We are what our microbiome eats.

Diverse List of High Fibre Foods - provide a source of prebiotics and bulk eg Vegetables and fruits (all colours), psyllium, flaxseeds, chia seeds 

Fermented Foods provide beneficial probiotics - Sauerkraut, Kimchi, Kefir, Kombucha. Pickled vegetables

Natural Anti-microbials - Apple Cider Vinegar, garlic, onions, fresh herbs

Super foods which are anti-inflammatory - berries, avocado, olive oil, 


Processed Foods, Fried Foods, Sugar, Alcohol, 



Diverse Meals


Be Outdoors

Interaction with pets

Limit exposure to pesticides, food chemicals, medications etc

Eat organic foods


Short Chain Fatty Acid supplements - Butyrate, Propionate and Acetate

Additional supplemental Fibres - Psyllium,  Flaxseeds


Understanding the relationship between specific foods and Autoimmune disease is very important.  Oral tolerance failure triggers immune reactivity against dietary antigens, which may trigger or worsen autoimmune disease when the food antigen shares homology of amino acids with human tissues.  Examples of the connection between Autoimmunity and food antigens include: Patients with rheumatoid arthritis report worsening of symptoms and also elevated IgG, IgA and IgM antibodies against food proteins such as milk, wheat, eggs, fish, pork, lectins and agglutinins.  Across 27 countries,  occurrence of Multiple Sclerosis correlated with consumption of cow's milk.  A recent systemic analysis of foods linked to Autoimmunity found hundreds of peptide epitopes that share homology with human tissue antigen.  Foods commonly associated with Autoimmunity and common sources of food allergens:






Nightshades - Contain alkaloids that tend to be inflammatory for some people.  However these wont show up on a food sensitivity test. Therefore its good to avoid the food to see if it is helping you. Some have genetic susceptibility to the alkaloid binding mechanism leading to inflammation. Nightshades include white potatoes, eggplant, tomatoes, bell peppers, paprika, red pepper flakes, cayenne pepper.

Lectins - Lectins are carbohydrate-binding proteins that can cause problems with digestion, absorption of nutrients, intestinal damage and moreover for autoimmune patients they can directly activate the TH17 response, especially those with Lupus and Rheumatoid Arthritis.  In lectins agglutination occurs where different proteins stick together to form a new antigen and the immune system reacts to this.  This is particular to certain genotypes.  Lectins can be deactivated by heat and soaking but there is no guarantee this will be a complete process. Examples include: Legumes (beans, chickpeas, lentils, peas, soy, beans), Nuts and Seeds (Almonds Cashews Sunflower seeds sesame seeds), Grains (Wheat, rice, buckwheat, quinoa, millet), 

Food Sensitivity Lab Testing allows you to see which foods you may be reacting to by producing antibodies to those foods and can be useful to focus on those foods rather than follow an elimination diet.  Studies have shown positive results with the paleo diet in Autoimmunity which eliminates dairy, gluten and grains.

An autoimmune diet may include:

• Vegetables and fruits

• Fermented foods

• Healthy oils (olive oil, avocado oil, flax seed oil)

• All meats

An autoimmune diet may eliminate:

• Gluten

• All grains - Rice, Oats, Tapioca, Quinoa, Millet, 

• Dairy​

• GMO proteins, Corn, Soy

• Lectins (Seeds, Nuts, Legumes) and Nightshades (Tomato, Potato, Eggplant, Peppers)

Efficient digestion of food is very important in Autoimmunity, if food is left undigested and it passes through a leaky intestinal barrier, immune cells may start to upregulate, causing food sensitivity and Autoimmune flares.  People can digest foods poorly for a variety of reasons, including aging.  Sufficient stomach hydrochloric acid and enzyme activity  is essential to break down food proteins as soon as possible so they don’t provide target sites for antibodies.  Hydrochloric acid is vital for digestion of proteins.  Proteins are made up of chains of amino acids, the building blocks of protein. Enzymes are necessary to break apart these chains of amino acids so the dendritic cells don’t become overwhelmed by proteins that are not completely digested. Effective digestive enzymes include pepsin, bromelain, proteases, and more.  A high-quality, broad-spectrum digestive enzyme supplement and HCL supplements may be required in certain people to aid digestion.


Low glucose levels in blood such as hypoglycaemia or Insulin resistance with low glucose in the cell can both generate a glycaemic response with up regulation of the cytokine IL6 which can drive inflammation and Autoimmunity.  

Normal Glucose response

  • wake up with energy and feel rested

  • wake up with an appetite

  • hunger between meals but no sugar cravings

  • no change in function between meals

  • no fatigue or change in energy after meals.

Functional Hypoglycaemia 

  • wake up with difficulty

  • no appetite in morning

  • consume caffeine or sugar for breakfast

  • lose function between meals 

  • energy after meals

  • crash around 3-5pm with sugar, salt, and caffeine cravings

  • difficulty staying asleep through the night

  • lightheaded if meals are missed

  • jittery, shaky, agitated, easily upset, nervous, poor memory, forgetful, blurred vision, fatigue, Insomnia, depression, mood disorders

  • slow metabolism, headaches and hormone imbalance.

It is very important to stabilise blood sugar levels throughout the day.  This can be done by eating high fibre, good fats and protein sources, eating more frequently through the day and avoiding high-glycaemic foods.

Insulin Resistance

  • wake up not feeling rested or recovered

  • wake up with sugar cravings

  • eat high sugar and high starch breakfast

  • sugar cravings all day

  • fatigue after meals

  • crash after lunch

  • need stimulants after meals

  • difficulty falling asleep

  • difficulty losing weight

  • need sweets after meals

  • fatigue, joint pain, depression or mood disorders, thinning hair, hormone imbalances.

It is very important to cut down on sugars and starches and increase exercise to stop fatigue after meals.  Many people are able to manage their high blood sugar and insulin resistance by following a low-carb or ketogenic diet and with intermittent fasting. The focus is on low GI foods, healthy proteins and fats and a diversity of fibre. Regular exercise is also vital to sensitise insulin receptors.


New research is showing that salt can be a factor in Autoimmunity by activating IL17 and TH17 pathways.  Doesn't affect all but can be an issue in some.  Research shows high-sodium foods can trigger Autoimmune flares in some people, particularly in those with high-blood pressure. Have you noticed if your symptoms are worse after eating salty foods?

High salt foods to avoid - 

Processed foods, bread & rolls, pizza, sandwiches, cold cuts and cured meats, soups, popcorn, crisps, snack mixes.


Chronic Gastro Intestinal symptoms such as diarrhoea or abdominal pain or inflammatory bowel disease may coexist with Autoimmunity.  Or there may be no gut symptoms but a leaky gut may still exist, especially if multiple food sensitivities are present. Therefore improving a leaky gut will improve oral tolerance and reduce sensitivities and up regulation of the immune system.

The basic leaky gut diet

This diet includes:

• Vegetables and fruits

• Fermented foods

• Rice and gluten-free grains

• Healthy oils (olive oil, avocado oil, flax seed oil)

• All meats

This diet eliminates:

• Gluten

• Dairy

• Processed foods

• Fast foods

• Fried foods

Some people have severe leaky gut which requires a more intensive dietary approach for repair.

This is also a foundational Autoimmune diet.

This diet includes:

• Vegetables and fruits

• Fermented foods

• Healthy oils (olive oil, avocado oil, flax seed oil)

• All meats

This diet may eliminate:

• Gluten

• All grains - Rice, Oats, Tapioca, Quinoa, Millet, 

• Dairy

• Whey

• GMO proteins, Corn, Soy

• Nightshades - Tomato, Potato, Eggplant, Peppers

• Lectins - Seeds, Nuts, Legumes

Compounds that support leaky gut:

• Bone broth

• Short-chain fatty acids (SCFAs)

• L-glutamine

• Vitamin D

• Probiotics

• Deglycyrrhizinated licorice (DGL)

• N-acetyl glucosamine

• Marshmallow extract

• Slippery elm

• Brush border enzymes

• Zinc carnosine 


Lab testing can help to identify any fungi, bacteria or virus that may have triggered and/or is still driving an overactive immune response.  Once identified, medications from GP or anti-microbials can help to eliminate the pathogen, depending on what it is.  Some anti-microbials that have been proven to work are:

Compounds to support intestinal fungus and yeast:

• Undecylenic acid

• Uva Ursi

• Cat’s claw

• Pau d’arco

• Tea tree oil

• Oil of oregano

• Lemon grass 

Compounds to support intestinal parasites:

• Wormwood

• Black walnut

• Olive leaf

• Garlic extract

• Oregano oil

• Goldenseal

• Barberry extract

Promote IFNg cytokine and Natural Killer cells to support your immune system ability to clear pathogens.  This can be done with black currant seed oil, sulforphane and andrographis.  

Promote TH1 response using berberine, to drive your immune system to kill pathogens especially if already TH2 dominant.


There is now compelling evidence that deficits in T Regulatory cells (TRegs) can lead to Autoimmunity.  TRegs suppress other T cells and immune cells using various mechanisms to maintain self tolerance and regulation during the immune response.  Some factors that have been researched to increase the number and/or function of TReg cells are as follows:

  • Vitamin D: Vitamin D3 supplementation is associated with significantly increased % of TRegs in apparently healthy individuals. This immunomodulatory effect of vitamin D might underlie the associations of vitamin D deficiency and autoimmune diseases.

  • Exercise: high-intensity training causes an increase in the proportion of regulatory T cells, as opposed to the effect of non-strenuous exercise on the TReg cell ratio.  

  • Omega-3 fatty acids: The promotion T cell differentiation into TRegs by dietary omega-3 fatty acids has been successfully proved to reduce the severity of diseases.   A healthy balance of omega-3 and omega-6 essential fatty acids is necessary for healthy TReg cell function. Most people get too much omega 6 oils through processed foods. A healthy dietary intake of omega-3 is 3500 mg for a person eating 2,000 calories per day. In addition to dietary sources, fish and algae oil are supplement sources of omega-3.

  • Short chain fatty acids (SCFA): Commensal microbes modulate the immune system in the colon through short-chain fatty acids, which induce TRegs.  Improving microbiome diversity is very important to increase SCFA production or alternatively, SCFA supplementation is good for those whose produce consumption is limited due to Small Intestine Bacterial Overgrowth (SIBO) or other digestive factors. 

  • Endorphins: there is a reciprocal interaction between the immune system and endogenous opioids (from exercise, laughter, positive relationships, volunteering, etc.) are a way to dampen inflammation and modulate the immune system.

  • Fasting: Fasting increases the TReg pool in mice and also diminishes the inflammatory response.  If there is significant self tissue debris due to chronic inflammation, then fasting can be considered.

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