Auto-Immune Diet by Sue Kira

by sue

Diet for Auto-immune conditions

by Sue Kira, Naturopath & Clinical Nutritionist

Introduction to Auto-Immune conditions

  • Different auto-immune conditions that can be supported by diet
  • Biomarkers that can be tested for auto-immunity
  • Auto-immunity, genetic susceptibility and foods
  • Contributing factors to auto-immunity

Foods to avoid with auto-immune diseases

Case study 1: Using diet for Auto-Immune Rheumatoid Arthritis

Case study 2: Hashimotos balanced by diet

Case study 3: Celiac diagnosis and treatment helps depression

Introduction to Auto-Immune conditions

The term Auto-Immune (AI) literally means self-destruction. It is where the body’s own immune system attacks itself rather than attacking foreign entities like bacteria, yeasts, fungi etc.

There is no clear scientific reason why this occurs, but the bottom line is that if you have an auto-immune condition, then your body is on self-destruct mode creating all sorts of trouble.

Food we eat is either harming or healing, inflammatory or anti-inflammatory. Could the self-harming choices of foods we eat undermine our health and wellbeing to the extent that the body starts to self-destruct? Yes, that’s indeed possible.

Following we look at aspects of auto-Immune disease and consider ways that you can eat your way back to health, along with the support of your doctors and health practitioners. Click for more information about Our Amazing Immune System – it’s great (if I say so myself).

Different auto-immune conditions that can be supported by diet

Here is a list of some auto-immune diseases that can be supported by an auto-immune diet under the advice and care of your health practitioner/doctor/specialist.

  • alopecia areata
  • autoimmune hemolytic anemia
  • autoimmune hepatitis
  • celiac disease
  • dermatomyositis
  • diabetes (type 1). Note: type 2 may be redefined as auto-immune soon
  • some forms of juvenile idiopathic arthritis
  • glomerulonephritis
  • Hyperthyroid/Graves’ disease (overactive thyroid)
  • Guillain-Barré syndrome
  • Granulomatosis with polyangiitis (Wegener’s)
  • Hashimoto’s thyroiditis
  • idiopathic thrombocytopenic purpure
  • inflammatory bowel diseases such as Crone’s and ulcerative colitis
  • lupus (Systemic Lupus Erythematosus – SLE)
  • myasthenia gravis
  • some forms of myocarditis
  • multiple sclerosis
  • pemphigus/pemphigoid
  • pernicious anemia
  • polyarteritis nodosa
  • polymyositis
  • primary biliary cirrhosis
  • psoriasis
  • rheumatoid arthritis
  • scleroderma/systemic sclerosis
  • Sjögren’s syndrome
  • some forms of uveitis
  • vitiligo

Biomarkers that can be tested for auto-immunity

Blood tests are essential when testing for auto-immune conditions, because they provide various biomarkers (biological markers) which are measurements of biological conditions within the body.

These biomarkers have the potential to….

  • diagnose even before onset of symptoms
  • predict or monitor response to diet and therapies
  • predict organ or tissue damage location and involvements
  • predict disease flares
  • identify potential disease sub-sets

Having these tests at the start, and then later when your symptoms have cleared, or six months have passed (whichever is the greater time) is appropriate. Your practitioner can interpret the results for you and may suggest further ongoing testing.

Test results show whether your biomarkers are within the acceptable reference zone or not. If your levels are borderline or slightly elevated, then there is an increased risk that you have, or will contract, a specific disease related to that marker. The tests are an excellent way to keep tabs on the weak links in your body.

For example, even though you may have one type of auto-immune disease diagnosed by your doctor, it is common for people to also have auto-antibodies attacking other parts of your body at the same time. It’s possible that if more tests are not conducted and these problems are left unchecked, then it is more likely that you can develop other auto-immune conditions simultaneously. Biomarkers provide clues to various conditions and other areas of your body you need to take care of.

You may find that your symptoms have cleared and think that you have healed. Yet through progressive testing, your practitioner can see if your health has improved on a clinical level. Without this knowledge, if you don’t know whether you have truly healed you could make the mistake of eating foods that might harm you.

Also, it can take many years for a disease to manifest symptoms, so just looking out for symptoms is not enough. Once you have had an auto-immune disease you are more prone to it occurring again, even in a different part of your body.

After initial tests, there is no imminent need to retest for those biomarkers that were shown to be within the accepted reference range. It’s only necessary to re-test for biomarkers outside the reference zone.

For this reason, I am placing a list of auto-immune tests that can be done. Some doctors won’t test all of them as it may cost the medical system too much money. However, it can be worth doing these with private laboratories via a naturopath or integrated doctor, even if you have to pay for them yourself, it is worth the peace of mind.

In some countries, these tests may not be available but it is still worthwhile to investigate which ones you can get done, particularly if you have some symptoms that don’t seem directly related to your condition.

Multiple autoimmune reactivity screen list

  • Parietal cell + ATPase antibodies: hydrochloric acid production
  • Intrinsic factor antibodies: for B12 absorption
  • ASCA and ANCA antibodies: marker of Crohn’s and Celiac disease
  • Tropomyosin antibodies: indicates cellular transformation into cancerous cells
  • Thyroglobulin and thyroid peroxidase: thyroid antibodies
  • 21 Hydroxylase: adrenal gland autoimmunity that can lead to Hashimotos, Addisons, Graves disease and vitiligo
  • Myocardial Peptide and alpha Myosin: associated with cardiomyopathy, myocarditis and rheumatic heart disease
  • Phosphoipid antibodies: cardiovascular dysfunction, endocrine dysfunction, recurrent miscarriage
  • Platelet glycoprotein: cardiovascular dysfunction
  • Antibodies to ovaries and testis: sex gland specific antibodies that can lead to premature menopause, ovarian failure and endometriosis
  • Fibulin, collagen complex and Arthritic peptide antibodies: associated with atherosclerosis.
  • Osteocyte antibody: marker for inflammation in the bones and osteoporosis
  • Cytochrome P450 Hepatocyte antibodies: liver antibodies creating inflammation that can lead to diabetes, hepatitis, cancer, kidney disease, peptic ulcers, epilepsy and congestive heart failure
  • Insulin and Islet cell antigens: type 1 diabetes predictor
  • Glutamic Acid Decarboxylase: antibodies to your brain (which can respond to a gluten free diet)
  • Myelin basic protein: associated with MS (multiple sclerosis), autism, lupus, and PANDAS (pediatric auto-immune neuropsychiatric disorders)
  • Asialoganglioside GM: brain antibodies similar to above
  • Alpha and Beta tubulin antibodies: nerve function
  • Cerebellar antibodies: against the brain, associated with shrinking brain often from gluten and inflammation in the brain
  • Synapsin antibodies: regulation of neurotransmitters and demyelination disease like MS, lupus, mood disorders and depression
  • Also, some labs do a ‘multiple autoimmune reactivity screen’

These tests provide the practitioner with biomarkers, to determine various biological conditions within the body.

However, if you simply cannot get these done then you can look at external markers. These are measurements or comparisons that we can see or feel, such as reactions to various foods and substances and your physical symptoms, such as skin condition, energy levels, hair loss etc.

An ideal way to observe all your current symptoms, even the small ones, is to use a diary to keep track of your symptoms and general health condition. It’s advisable to complete the information before you change your diet, medication or supplementation. Then regularly complete the information, including any changes to diet etc to see how you are progressing. Any new symptoms or symptoms that don’t go away need to be discussed with your practitioner.

Auto-immunity, genetic susceptibility and foods

Auto-immune conditions are commonly considered to start with a genetic susceptibility, but the genes responsible must be triggered or ‘switched on’ by lifestyle, food choices and environmental factors which then instruct your genes how to be expressed.

The foods you eat or don’t eat, your stress levels, sleep habits and exposure to toxins are all factors that help determine your genetic expression. When it comes to auto-immune conditions, once that genetic switch has been turned on, it usually doesn’t turn off again, but the autoimmune response can be dampened tremendously by diet, lifestyle and other possible contributing factors.

Some say they have been cured of auto-immune disease by changing their diet. Others call this a remission. Irrespectively, if you can alleviate your systems and stop your body from destroying itself, then that’s a winner.

Contributing factors to auto-immunity

Other contributing factors that can affect the auto-immune response are:

  • the health of your gut and if you have leaky gut or SIBO (Small Intestine Bacterial Overgrowth)
  • food intolerances and allergies. Many foods such as gluten can really create issues with auto-immune conditions, even if you don’t have celiac disease (which is an auto-immune disease)

As mentioned, if you have one auto-immune disorder, then you are more susceptible to others.

For those with AI disease, it’s important to keep an eye on antibody levels in the blood, as this is an indicator of how bad the condition is at any given time, or if there are other antibodies appearing, related to other types of AI conditions.

Foods to avoid with auto-immune diseases

Regarding foods that are best to avoid, gluten is by far the worst culprit.

Gluten is inherently inflammatory, stimulates the immune system (in a bad way), feeds the wrong bacteria into the gut and is damaging to the lining of the gut – creating what is termed ‘leaky gut syndrome’ or intestinal permeability.

A study was done on a group of healthy 20+ year old University students. They were initially tested and all showed no gut conditions. They were given a MacDonald’s breakfast to eat and 65% of them tested positive for ‘leaky gut’ after consumption. Their elevated inflammation markers took two weeks to settle back to normal and clear.

Wow! Two weeks to clear the inflammation from just one meal full of gluten, processed foods and sugar. Microbiologist Dr Kiran Krishnan said that if adolescents ate these types of foods more than once a fortnight, then many are very likely to develop an auto-immune disease by the age of 30.

There are also other various potential problem foods that can create issues, which have been researched as incompatible with auto-immune conditions. These include: gluten; processed foods; sugar; all dairy products; grains; legumes; nuts and seeds; soy products, eggs, spices of seed origin; seaweeds; and the nightshade family of foods i.e. eggplants, tomatoes, potatoes and red bell peppers (capsicum) as well as the very high histamine foods. These foods are considered to create inflammation or leaky gut.

While an auto-immune diet is not considered a cure, it is one that includes foods that support the body, and eliminates foods considered detrimental, to help your body to do its natural job of healing. For that reason, an auto immune diet is free of gluten, dairy and additives.

There is a host of suitable nutritious foods that include: most organic vegetables; organic chicken, turkey, beef and lamb; fish and seafood; low sugar fruits; coconut products; and delicious herbs and certain spices (except for seed types and nightshade varieties).

You could call an auto-immune diet an anti-inflammatory paleo style diet with low histamine foods. Your health care practitioner may also consider conditions such as leaky gut, SIBO, sleep quality, stress support etc.

Important: Before you change your diet, see your medical or health care professional for qualified guidance and do not stop any medications or supplements previously prescribed unless advised otherwise by your medical or health care professional, who may even prescribe extra supplementation.

Note: During the early stages of a new diet, you may experience symptoms such as fatigue, headaches or body aches, which may occur because your body is detoxifying. However, if you are unsure about a symptom at any time, check immediately with your medical or health care professional.

Case study 1: Using diet for Auto-Immune Rheumatoid Arthritis

Client name and identifying information changed

Lucy came to me after she had struggled for years with the crippling pain of Rheumatoid Arthritis. Lucy was quite upset that she had been diagnosed with a condition in her 20’s that she thought was for the elderly. Now in her early 30’s Lucy was still suffering.

At first when she was diagnosed she was prescribed drugs that made all the pain go away and she was happy to live this way. But as the years went by, the drugs became less effective, and she was given more and more drugs to suppress the increasing pain.

Lucy asked the specialists if there were any foods that she should or should not be eating to help her deteriorating condition. She was told that there was no evidence of any foods being an issue or support, and was told to have a good balanced diet, including a glass of red wine to help relax her at the end of the day. After some thought and research Lucy felt this wasn’t right and came to see me.

I recommended bowel tests and food intolerance tests as I knew there was a strong link of leaky gut/intestinal permeability and imbalances in gut microbes and food intolerances to the health of the immune system.

The tests results showed that she had leaky gut and was intolerant to gluten, not strongly, but enough for me to suggest going 100% gluten free. Her inflammation markers were strong so we set Lucy up with an anti-inflammatory diet with no grains, sugar or alcohol. We also included an 80% plant based diet with 20% good fats and proteins.

Within four weeks her residual pain was gone and she had lots more energy and all markers had improved. After another couple of months on this diet, Lucy decided to gradually wean herself off her drugs to see if the pain would come back. This was not my recommendation but her choice to do so. She was very surprised and relieved to discover that she had no pain.

Lucy was reluctant to re-visit her specialist as she didn’t want to receive a ‘lecture’. But I convinced her to go and get her antibodies tested so she could be certain whether her condition had healed, or if she was in remission, or there was a placebo effect.

All tests came back clear. Now she doesn’t know whether she really had Rheumatoid Arthritis. But it didn’t matter as she was finally pain free after 15 years on drugs that did little but suppress her symptoms.

Lucy also mentioned that if she accidentally eats gluten then she wakes with terrible pain in her fingers. It was enough for her to commit to a gluten-free lifestyle.

Case study 2: Hashimotos balanced by diet

Client name and identifying information changed

Every now and then as a practitioner, I would get what I called the real ‘doozies’ – those cases where I wasn’t sure where to start, or if I could even help those clients because they had already been everywhere and seemingly covered every angle about their condition.

In recent years, these clients became more the ‘norm’ than the odd one out, or perhaps I attracted them because of my repeated success rates.

My rule of thumb with difficult health situations is, if in doubt, treat the gut and sort out the diet and then go from there. This case was no different.

When Lydia first saw me she had a folder of information, test results, scans and a list of symptoms, supplements and things she had done over the previous two years with doctors, naturopaths and other ‘healers’.

Lydia’s thyroid problem started about 2.5 years before she saw me, after she gave birth to her second child and then put on an enormous amount of weight (25kgs/55lbs) onto her slightly framed body. She was very tired and foggy in the head, which was put down to childbirth, being a new mum and not getting enough sleep.

Eventually one doctor found that Lydia had an underactive thyroid and put her onto thyroid replacement hormone and she thought all her problems would be solved. She did in fact feel a little bit better with more energy for a few months, but then all came crashing down again.

Back to the doctors and her TSH (Thyroid Stimulating Hormone) was through the roof and antibodies were very high, so her medication was doubled and again, she felt a little better for several months – but then back to square one.

This time the doctor sent her to a specialist where she had more tests and her medication was further increased. However, instead of feeling better with the higher dose, she felt worse – her heart rate was rapid, she had anxiety, couldn’t sleep, felt restless and generally unwell.

These were symptoms of an overactive thyroid, as if her thyroid levels had gone too far the other way. Yet tests revealed that her TSH was nearly normal (a bit low) but her antibodies were higher than ever. The doctor tried to lower her medication but then she became so tired and put on even more weight, to the point where she just didn’t know what to do.

After more tests and specialist appointments, Lydia was getting nowhere, felt worse and fed-up. That’s when she saw me.

Folder in hand and exhausted, she wanted me to look at her situation differently and hopefully help her. She said, “You’re my last resort, I just don’t know what to do anymore”.

I have heard these words so often from clients, and I would answer, “Never, never give up or you will stay the same or get worse. If not me, then someone else will be able to help you.”

After an initial overview of Lydia’s situation I decided to investigate her gut health, as many diseases physically start in the gut. (I say physically, because most health conditions are emotionally based, but then physically manifest somewhere in the body, often in the gut, and then continue a path of destruction to other organs.)

From some in-clinic tests, it looked like Lydia’s gut was unhealthy, so we organised some lab tests and sure enough, her digestive system was a mess.

She had loads of inflammation, high markers for gluten sensitivity, high markers for putrification in her gut and terrible levels of good and bad bacteria – too many bad, not enough good. Leaky gut (intestinal permeability) was also present and she had intolerances to many foods. Tests also confirmed low levels of vitamins and minerals, which indicated she was not absorbing nutrients efficiently.

Interestingly, Lydia was totally oblivious to her digestive system being such a mess, because she felt so bad in many other ways that it was all a blur of discomfort.

Because Lydia had been to many practitioners, doctors and specialists, her funds were low, so she didn’t want to take any supplementary products initially, but she had a strong feeling that diet changes might help. She had experimented with diet by randomly choosing to eliminate certain foods like gluten or dairy but never the two together, or any other foods.

Essentially, it was too exhausting for her, particularly because of how she felt and looking after a family. She needed guidance – that was my job.

Knowing Lydia’s case was quite serious because she was not responsive to medication and her immune system was attacking her body, I put her onto the full Auto-Immune diet protocol. There was no beating around the bush or going in gently, we dropped her in the deep, so to speak, with a radical change to her diet as we needed to reduce the inflammation pronto.

Normally I suggest to ease into these protocols by starting with a gluten, dairy and sugar free diet, but with so many intolerances and so much going on in Lydia’s body, we also included the second and third phase of the auto-immune protocol.

This involves avoiding all grains (not just the gluten ones), all nightshade family of fruits/vegetables, eggs, all fruits, nuts and all legumes. She was also placed on a low ‘FODMAPs’ diet combined with a low histamine diet. We also removed any foods that tested sensitive. All of this was combined.

This left Lydia with a very basic diet of proteins from meats, poultry and fish (all to be very fresh, thus low histamine) along with certain vegetables that are low FODMAPs and low histamine.

By taking away all potential inflammatory foods and aggravants to her body, within only three weeks Lydia felt much better. We still had a long way to go, but it was a good start. After another three weeks at this intensity. Lydia felt quite normal, but we needed to see her markers again.

Her thyroid (still on medication) was now within the normal reference level and her antibody levels had halved so we knew that even though she felt so much better, we still had work to do. Lydia was so pleased with how things were going that she was happy to continue with this restricted diet for another three months, after which we retested her antibodies and her gut.

Her antibodies were now within normal levels, so that meant no more auto-immunity for her thyroid and her TSH was dropping low enough for the doctor to drop her medication by half (he was very surprised).

She wanted to continue longer with this diet, but I felt it was time to re-introduce some of the foods that had been removed to see if any caused issues. It was time to ‘challenge’ her body.

I advised Lydia to gradually re-introduce only one food every three days and really feel if her body responded negatively to any foods. I suggested to commence with some of the foods she missed the most but leave out the foods on her reactive list till last.

Over the next three months Lydia managed to reintroduce many of the foods. She only reacted to three foods challenged and these were tomatoes, tinned tuna and chocolate. At this stage, we hadn’t challenged the more potentially dangerous foods like gluten, dairy, grains or eggs.

After 12 months on the less restrictive diet, we tested again and it looked like her thyroid condition had never existed and by this stage she was off medication. Her weight was normal, her energy good, she was sleeping well and she was so pleased that she found something to help her ‘get her life back’.

There were only three foods she hadn’t challenged which were grains, dairy and eggs. Before doing anything about these foods I asked her to get another food intolerance and allergy test done. Gluten, dairy (both casein and lactose) and egg whites all still came up reactive (yolks were ok).

I suggested to Lydia it would be best for her not to ever eat these reactive foods again. I would like to add that once we knew Lydia was fine with histamine foods, we also introduced gut healing foods like fermented probiotic rich foods and bone broths to help heal her gut and re-establish good bacteria.

It’s quite possible that the stress of her second childbirth, poor eating habits and potential intolerances, set off a leaky gut that cascaded into her initial auto-immune disease spiral of ill health.

However, along the way when Lydia came in for check-ups, we also discussed potential emotional triggers for her condition. We spoke about how thyroid conditions can be linked to holding back something we need to express and how we over-ride what we feel is best. Also, the intestines are generally about self-worth.

With these cues, she told me that when she gave birth to her second child, a feeling of dread came over her when she was to go home, because she knew she wasn’t going to get any support from her husband. It was bad enough with the first child but worse now there were two children. She didn’t respect herself enough to voice her concerns and she bottled it all up inside, only to be expressed through her body going into self-destruct mode.

She was right about not getting the help needed, but the worst part was that she didn’t even ask for help. Many women tend to ‘martyr’ themselves, thinking that their loved ones should just know to offer help. Meantime, their partner thinks all is well and each has their different roles in the house. I’ve made the same mistake myself in the past, so I could share how I managed to change this situation.

Lydia’s situation could have ended in divorce, so she needed to resolve it or risk creating another disease. Thankfully her husband was very open to do more in the home; he actually thought that Lydia was happy to do everything. He did need a nudge every now and then, but they were both much happier with improved communication.

Does this mean that all Hashimoto’s disease cases can be reversed by diet and talking to your partner (or whoever)? Not necessarily…but it’s worth a try.

Case study 3: Celiac diagnosis and treatment helps depression

Client names and identifying information changed

Caleb was so sick that he couldn’t make it to the clinic for his first consultation, so I first saw him via skype. He had gut pains, body aches, diarrhoea, foggy head and depression. The depression bothered him the most as he was unable to work and could barely function.

Even though he was 48 at the time, Caleb had to move in with his mother so she could look after his cooking. Mum Janet was very stressed and worried about her son and was committed to doing what was needed to get him better as soon as possible.

We ran some tests and he had ‘leaky gut’ which was quite bad, multiple mineral deficiencies in vitamin B6, B12, Iron, vitamin D and he tested positive for celiac disease. He already had a strong feeling that he had an issue with gluten foods, but because he was so exhausted, he often ate two minute noodles until he moved back to his mother’s house.

He also drank copious amounts of chocolate milk when he didn’t have much energy, as it was easy and filling, but the milk also tested reactive, along with most of the gluten cross-reactive foods and a few others. His system was so sensitive that every time he tried to take any vitamins he would feel too sick, so we just needed to work with food to get Caleb feeling better.

Once we knew what we were working with, Caleb and Janet were instructed to go 100% Gluten free and to also be totally free of all the cross reactive and other reactive foods. We couldn’t risk any gluten or reactive foods in the entire house in case of any cross contamination, even down to checking all personal care items for gluten.

That might seem strange, but did you know that wheat protein is used as a thickener in many products like shampoo and creams? They all had to be checked and removed from the house.

I put Caleb onto a diet that was not only reactive food free, but also included foods that would help to heal his leaky gut and damaged microvilli, as well as being rich in nutrients to re-build his deficiencies. Initially we started with some basic bone broths to help settle the inflammation in his gut. The broths felt very calming to Caleb’s digestive system and his nervous system.

He didn’t have much energy from the broths alone, but he was happy to sleep a lot while his body healed. It took about a month to settle his system from the inflammation. Then we added some good fats to build up his calories and give the body more healing nutrients to help him to feel better mentally and emotionally.

We also gradually added in slow cooked meats to the bone broths and some low fibre vegetables. Note: fibrous vegetables can further inflame an already inflamed, irritated, damaged gut lining.

As Caleb’s energy and appetite gradually increased, he added more meats and a broader range of vegetables (leaving the fat on his meat cuts). He ate low inflammation foods and stayed off foods he was reactive to, as well as foods from the nightshade and brassica families and all legumes, to keep it simple for his digestive system.

Then after a month, with Caleb’s recovery going well, we introduced some small quantities of coconut milk/cream/yoghurt and oil (all unsweetened plain at this stage) plus sweet potato which he craved. Caleb was gradually getting better every week and by about four months he was eating a full range of foods except for the known reactive foods.

We left these out for 12 months and then tested him to see what was reactive. At that point only quinoa and rice showed reactivity, along with gluten and dairy which will probably never be appropriate for him again.

Caleb left all reactive foods out of his diet for about 14 months as this felt right for him. He then re-introduced one at a time, feeling his body for reactions and energy drops, and he found he was fine. He did sneak in some dairy one day and felt so bad energy wise that he didn’t have it again.

It can take two to three years for a gut to heal from celiac disease, and Caleb was no exception. He had a stool check and a colonoscopy with biopsy after two years and he was nearly completely healed with back to normal microvilli. Inflammation markers in the gut were all good and his bacteria levels were reasonable.

It took a lot of work for Caleb to get back to where he felt ‘normal’ again, but it was well worth it.

After his initial 12 months of working with just the diet, his sensitivities were not so bad, so we introduced some probiotic bacteria to increase his levels of good bacteria (the ‘good guys’) along with some zinc and vitamin D supplements as he wasn’t getting much sun and his zinc levels weren’t increasing enough with the diet to help to fully heal his gut. It was great that he could tolerate the supplements.

He didn’t like to eat fish so we also used some Omega fats to support his mental health. The combination of the above in the right sequence, worked to get Caleb feeling better physically, mentally and emotionally and he was back at work after 12 month’s recovery.

I had many clients who recovered faster, but Caleb was in a bad way and probably had celiac disease for some time, but ignored the symptoms until his body couldn’t take any more.

It pays to listen to your body and get checked early, without delay.


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