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Autoimmune disease protocol diet (AIP) and how nutrition and gut health can assist with symptoms

Autoimmune disease protocol diet (AIP) and how nutrition and gut health can assist with symptoms

Autoimmune disease protocol diet (AIP) and how nutrition and gut health can assist with symptoms

In contemporary society, more and more people are finding that underlying their chronic health conditions is an autoimmune disease and impaired gut health.  There are strong links between Autoimmune disease and Gut Health.

Autoimmune diseases have a strong link to the state of our gut health. With a Functional Medicine approach, you can learn how to reduce your symptoms, recover from autoimmunity and live your best life, full of energy and free from pain.

What is an autoimmune disease?

An autoimmune disease (AID) is a condition in which your immune system mistakenly attacks your body. Your immune system fights off bacteria and viruses with an army of fighter cells to attack them. Usually, the immune system can tell the difference between foreign cells and your own cells. 

In an immune system disease, however, the immune system mistakes part of your body as foreign in a process called molecular mimicry.  This process releases proteins called autoantibodies that attack healthy cells that have been mistaken as foreign invader cells.

The exact cause of an autoimmune disease is poorly understood but seems to be caused by a combination of genetic, environmental, hormonal and immune factors. Much of our genetics are expressed by our environment, meaning our diet and lifestyle have the biggest impact on our genes. 

When compromised individuals are exposed to certain environmental triggers, such as microorganisms or toxins, the following occurs:

Environmental triggers produce inflammatory cytokines activate T helper cells including Th1 and Th17 immune attack on body by self-antigens.

Gut Health and Autoimmune Disease

The long term state of our gut health greatly influences the chances of developing an autoimmune disease and progression of the disease if you have already developed one.

There are strong links with regards to the integrity of the intestinal lining and mucosa barrier, two key factors in gut health. When the tight gap junctions in our intestinal lining are compromised large protein and food particles are able to flood into the blood stream. This unwanted process fires up the immune system and activates inflammation cascades.

Long term dysfunction in this area leads to an increase in the chance of developing an autoimmune disease.

Clinically, we find many of our autoimmune patients have intestinal permeability, a parasitic infection of bacterial overgrowth or a severely depleted amount of beneficial bacteria.

Autoimmune disease and gut health are strongly linked, gut health should be a key part of any autoimmune condition treatment.


Defective T cells don’t stop the attack → increased inflammation → increased antibody production → tissue damage and attack on healthy cells.

Types of autoimmune disease

Autoimmune diseases are a group of chronic inflammatory conditions, some targeting only one organ and others affecting the whole body.

There are over 80 different types of autoimmune diseases with many other known diseases suspected to have an autoimmune component to them. 

Autoimmune disease symptoms will depend on the organs or tissues affected. Autoimmune disease and gut health are connected in nearly all of these conditions. Examples of autoimmune diseases include: 

Alopecia areata

Loss of hair from some or all of the body, mainly the scalp

Ankylosing spondylitis

Affects the joints of the spine and sacroiliac joint, causing fusion and rigidity, which in turn causes back pain, reduced mobility in the spine and stiffness

Antiphospholipid syndrome

Provokes blood clots in arteries and veins. APS is a disorder of coagulation which can be a primary diagnosis or secondary to lupus. Symptoms include deep vein thrombosis (DVT) which appears as pain, swelling and redness. People with APS may also experience repeated miscarriages or stillbirths, stroke, transient ischemic attack (TIA) or rash.


New research is suggesting that autism may be autoimmune in origin. It is “a spectrum of behavioural anomalies characterized by impaired social interaction and communication, often accompanied by repetitive and stereotyped behaviour.” 

Chronic fatigue syndrome / fibromyalgia

Possibly autoimmune in origin. Both are characterised by a lack of energy and in the case of fibromyalgia, pain. 

Autoimmune disease

Celiac disease

Affects villi of small intestine. Symptoms include diarrhoea, bloating, cramps, gas, fatigue, weight loss, constipation and depression.

Crohn’s disease

Inflammatory bowel disease affecting entire colon wall, mostly the lower ileum. Crohn’s disease is characterised by diarrhoea, fever, fatigue, abdominal pain and cramping, blood in the stool, mouth sores and reduced appetite and weight loss. 

Dermatitis herpetiformis

Affects skin, particularly elbows, knees, back and neck; associated with celiac disease. It is a chronic skin condition associated with coeliac disease. It is intensely itchy, even when only appearing as a mild rash.

Type 1 Diabetes

Affects pancreatic beta-cells causing insulin deficiency. Symptoms may appear suddenly and can include increased thirst, frequent urination, extremely hunger, irritability, fatigue, weakness and blurred vision.

Goodpasture’s syndrome

A rare but serious autoimmune disease that affects kidneys and lungs. Symptoms include nose bleeds, pallor, a cough and breathing difficulty. 

Grave’s disease

Affects thyroid gland, causing hyperthyroidism (overactive thyroid). Symptoms include anxiety and irritability, a fine tremor in hands or fingers, heat sensitivity and an increase in perspiration or warm, moist skin, weight loss, enlargement of the thyroid gland, change in menstrual cycles and bulging eyes.

Guillan-Barre syndrome

Affects the peripheral nervous system, attacking the nerves in the legs, arms, and upper body. Weakness and tingling in your extremities are usually the first symptoms. These sensations can quickly spread, eventually paralysing the whole body.

Hashimoto’s thyroiditis

Affects thyroid gland, causing hypothyroidism (underactive thyroid). Symptoms include weight gain, fatigue, paleness or puffiness of the face, joint and muscle pain, constipations, inability to get warm and difficulty getting pregnant.


Affects the skin, joints, kidneys, lungs, heart, brain and blood cells with symptoms varying from person to person. Lupus symptoms include muscle and joint pain, fever, hair loss, chest pain, kidney problems, mouth sores, rashes and sun or light sensitivity.

Multiple sclerosis

Affects myelin sheath in neurons of the brain and spinal cord. Early signs include vision problems, tingling and numbness, pains and spasms, weakness or fatigue, balance problems or dizziness, bladder issues, sexual dysfunction and cognitive problems.

Myasthenia gravis

Affects muscles, especially those around the eyes. Some of the symptoms include weak muscles, visual disturbances such as double vision, inability to hold a steady gaze and droopy eyelids, fatigue, swallowing and/or difficulties and shortness of breath.

Parkinson’s disease

Affects dopamine-generating cells in the central nervous system. It causes trembling in the hands, arms, legs, jaw, and face; rigidity or stiffness of the limbs or trunk; slowness of body movements; and unstable posture and difficulty in walking. 

Pernicous anaemia

Affects parietal cells in the stomach, leading to the inability to absorb Vitamin B12 and creating a deficiency. Symptoms include vomiting, heartburn, abdominal bloating and gas, constipation or diarrhea, loss of appetite and weight loss.


A common skin condition that affects keratinocytes. The life cycle of skin cells is sped up and the extra skin cells form scales and red patches that are itchy and sometimes painful. 

Rheumatoid arthritis

Musculoskeletal disorder affecting connective tissue in joints. Early signs include fatigue, a slight fever, weight loss, stiffness and joint tenderness, pain, swelling and redness.


May be triggered by autoimmune reaction in brain cells. It is a significant mental illness that causes someone to have an altered experience of reality. 

Sjogren’s syndrome

Affects exocrine glands, primarily the salivary and lacrimal glands. It is identified by its two most common symptoms — dry eyes and a dry mouth. The condition often accompanies other immune system disorders, such as rheumatoid arthritis and lupus. 


A general term that refers to inflammation of the thyroid gland and can include diseases such as Hashimoto’s and Grave’s.

Ulcerative colitis

Inflammatory bowel disease, affecting mucosa of large colon. Symptoms include diarrhoea, blood or pus in the stool, fever, weight loss and abdominal pain and discomfort.


Affects melanocytes resulting in the loss of skin colour in blotches 

Why are autoimmune diseases becoming more common?

The global incidence of autoimmune disease has significantly increased over the past 20 years and has more than tripled in Australia in the last decade. It currently affects around 5% of people in Australia, with females accounting for 75% of those affected. 

So, why is this the case?

Nutritional factors, gut dysbiosis, environmental toxins and stress. 

Our increased consumption of commercially farmed and processed foods and drinks, combined with a decline in the quality of food we eat, are having a major toll on our health. 

Our gut health is poor, leaving us with compromised digestives systems which over time, cause intestinal permeability. This is also known as ‘leaky gut’ in which the intestinal lining is damaged, food proteins pass through into the bloodstream that should be contained in the gastrointestinal tract.  

These food proteins pass through the compromised tight gap junctions in the small intestine and flood the immune system with molecules that are foreign to the immune system. 

Over a period of time, this continual presentation can cause the immune system to become confused and incorrectly mark a healthy cell as a foreign invader (molecular mimicry) starting the process of autoimmune disease.

How can we treat autoimmune disease?

As Functional Medicine health professionals, the first thing we look at is how the gut and digestive system are working through the comprehensive testing of and for:

  • Blood chemistry
  • Auto-antibodies
  • Intestinal permeability 
  • Advanced stool testing
  • Small intestinal bacterial overgrowth (SIBO) 
  • Mineral analysis
  • Key vitamins including D3 & B12 
  • Pathogens  
  • Metabolism

Once we have a clear picture of your state of health, we can begin to treat your digestive and associated body systems to regulate your immune response.

Nutrition and autoimmune conditions 

The Autoimmune Paleo Diet (AIP), also know as the Autoimmune Protocol Diet, focuses on avoiding foods that cause inflammation in your body. The major antigens found to be linked to autoimmune diseases are gluten and casein. The diet also removes nightshades, eggs, nuts, seeds, ghee, and caffeine, in addition to standard paleo restrictions.

Foods to eat on the AIP diet include:

  • Meat and fish, preferably not factory raised
  • Vegetables (but not nightshades, such as tomatoes, eggplants, peppers, and potatoes)
  • Sweet potatoes
  • Fruit (in small quantities)
  • Coconut milk
  • Avocado, olive and coconut oil
  • Dairy-free fermented foods, such as kombucha, kefir made with coconut milk, sauerkraut, and kimchi
  • Honey or maple syrup (but only to be used occasionally, in small quantities)
  • Fresh, non-seed herbs such as basil, mint, and oregano
  • Green tea and non-seed herbal teas
  • Bone broth
  • Vinegar such as apple cider and balsamic

Foods to avoid on the AIP diet include:

  • All grains, such as oats, rice and wheat
  • All dairy
  • Eggs
  • Legumes, such as beans and peanuts
  • Nightshade vegetables (tomatoes, eggplants, peppers, and potatoes)
  • All sugars, including sugar replacements (except for occasional use of honey)
  • Butter and ghee
  • All oils (except for avocado, coconut, and olive)
  • Food additives
  • Alcohol

With a serious autoimmune disease, patients will need to follow the Autoimmune Paleo Diet (AIP) strictly for some time. Once antibodies are reduced and healing in the intestinal tract has occurred, a Functional Medicine health professional may assist with the reintroduction of some foods. 

It is likely that some foods will need to be removed for a very lengthy amount of time. Food sensitivity testing can assist in this area. With the introduction of the Autoimmune Paleo Diet and other associated treatments, we regularly see excellent improvements in patients within just a few short weeks.

The diet and associated treatments will work towards:

  • Eliminating parasite, bacterial, fungal and pathogenic infections
  • Reducing intestinal permeability
  • Treating nutrient deficiencies
  • Reducing antigenic load (food antigens, toxins, pathogens) 
  • Reducing inflammation and oxidative stress 
  • Optimising intestinal microflora and promote intestinal repair 
  • Promoting tissue repair 
  • Supporting and correcting digestive and liver function 
  • Detoxifying your bowel and liver 

Stress management and autoimmune disease

At least half of autoimmune disorders are attributed to unknown factors, with physical and psychological stress being considered as a trigger for the onset of autoimmune disease.

“… many retrospective studies found that a high proportion (up to 80%) of patients reported uncommon emotional stress before disease onset. Unfortunately, not only does stress cause disease, but the disease itself also causes significant stress in the patients, creating a vicious cycle.”

Functional Medicine health professionals can help you, in collaboration with other supports such as counseling, to manage your stress through diet plans, balancing brain chemistry, nutrient therapy, and targeted herbal medicine.

An individualised approach is required to put autoimmune disease into remission.  Supplements that support autoimmune conditions include prebiotic/probiotic supplements, B12, curcumin, Vitamin D3, glutamine, and an antioxidants. A range of herbal medicine treatments is also beneficial in supporting the immune system and systemically treating autoimmune conditions.

How you can find the path to wellness

Functional Medicine health professionals aim to uncover the root causes of your autoimmune disease. We work with our patients to get a complete picture of their overall health and help you understand what your body needs to rebalance

Our approach entails a diet plan and nutritional advice, balancing your body chemistry and gut health through targeted supplements and herbal treatments

Fill out the below form or call us on 1800 11 22 36 to find out more .

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The above information is intended to be general, educational advice only, on topics which are of interest to us. It is not intended to represent specific or individual health or medical advice and is not specific to your situation. The below information is educative and is not intended to advertise any service.

Before making any decisions in relation to your health, you should always discuss your individual situation with your own health practitioners to ensure that any advice you have read is right for you.

Jarrod Cooper – ND

Jarrod Cooper – ND

Jarrod Cooper - ND is the founder of Advanced Functional Medicine Australia. He is a Naturopathic Doctor with extensive functional medicine training from leading practitioners in the USA and worldwide.

He is leading the way with advancements of functional medicine, clinically implementing worldwide best practices in Functional Medicine throughout Australia.

Jarrod consults in person from Perth, Western Australia and also online via Telehealth throughout Australia and worldwide.

If you are looking for personalised treatment, we highly recommend contacting Jarrod Cooper’s Advanced Functional Medicine clinic in Australia.

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