Leaky Gut Diet by Sue Kira

by sue

Diet for Leaky Gut (Level 1 & Level 2)

by Sue Kira, Naturopath & Clinical Nutritionist

About leaky gut (intestinal permeability)

Healing a leaky gut

Intermittent fasting to heal leaky gut

Histamine intolerance and leaky gut

The SIBO Diet (Phase 1 & 2)

The Leaky Gut Diet (Phase 1)

The Leaky Gut Diet (Phase 2) 

Case study: Healing leaky gut and depression naturally

About leaky gut (intestinal permeability)

Our digestive tracts are there to serve as a protective barrier between our blood stream and the food we eat, but at the same time, allow the absorption of fully digested fats, proteins and carbohydrates into our blood stream.

From the gut, these macro-nutrients are then absorbed into the blood via what are called ‘tight junctions’ which are the very small, tight joins between the cells in the gut lining which are butted up against each other.
But when the digestive tract gets affected by infections, inflammation, antibiotic use, chronic stress, environmental toxins or processed food, then the gut lining gets weak, those ‘tight joints’ start to separate, and the gut becomes more permeable or in other words ‘leaky’.

With a weak or leaky gut lining, we get larger undigested food particles into the blood stream. The immune system gets confused about these undigested food particles floating around and starts to launch immune responses against certain foods, creating food sensitivities. If left unchecked, additional immune responses can occur and eventually various diseases and disorders can eventuate.

Common symptoms & disorders related to Leaky Gut Syndrome
  • Allergies
  • Anxiety
  • Arthritis
  • Asthma
  • Autism
  • Autoimmune disease
  • Cancer treatments
  • Celiac Disease
  • Chronic fatigue syndrome
  • Constipation
  • Crohn’s disease
  • Cystic Fibrosis
  • Depression
  • Diarrhoea
  • Eczema
  • Ear Infections (recurring)
  • Environmental illness
  • Food sensitivities/allergies
  • Gas/bloating/wind
  • Hives
  • Hyperactivity
  • Indigestion
  • Irritable Bowel Syndrome
  • Learning and behaviour problems
  • Malabsorption/malnutrition
  • Multiple Chemical Sensitivities (MCS)
  • Parasites
  • Poor immune function
  • Psoriasis
  • Skin rashes
  • Ulcerative colitis

Healing a leaky gut

As you can see, leaky gut can be related to numerous health conditions, so it is important to get it under control as soon as possible.

If you have been diagnosed with leaky gut syndrome or feel you may have it then it is imperative to seek advice from your health care provider soon regarding some of the causes and concurrent imbalances such as possible infections, bacterial overgrowth, food intolerances, and also to get good nutritional, probiotic and gut healing support.

The most important thing to do to help your gut to heal and seal is to first remove the things that are damaging your gut and creating inflammation.

In my experience with clients over many years, the most success I have had to effectively heal leaky gut has been with dietary modifications, normally over a period of 3 to 6 months, depending on various factors.

Until the gut is completely healed (for which there are lab tests to confirm) it is best to stay away from certain aggravating foods. The next most important thing to do is ensure that you are eating plenty of anti-inflammatory foods and foods that help to heal the gut. (These foods are covered later in this article).

A diet for leaky gut diet is done in stages. Here’s an overview…

Step 1: Intermittent fasting
For those with mild symptoms, an intermittent fasting diet over 3 weeks is a good option to see if your symptoms improve and get you back on track. But if your symptoms don’t improve after 3 weeks, then go to either Step 2 or Step 2A, depending on your symptoms and/or disorders. If your symptoms are stronger than mild, then go straight to either Step 2 or Step 2A .

Step 2: Diet for Leaky Gut (Phase 1 & 2)
The Diet for Leaky Gut is 2 stages, normally over a total 3 month period. Phase 1 is to settle inflammation to allow the leaky gut to seal and heal. Phase 2 is to rebuild and re-seed the gut.

Step 2A: Diet for SIBO (Phase 1 & 2) then Leaky Gut (Phase 1 & 2)
At least 80% of my clients with Leaky Gut Syndrome also had  SIBO (Small Intestine Bacterial Overgrowth) which has to be cleared with a  SIBO Diet first over 3 months, before moving onto the Leaky Gut diet for 3 months.

This means that most people need a 4-phase dietary program over approximately 6 months i.e. SIBO Phase 1; SIBO Phase 2; Leaky Gut Phase 1; Leaky Gut Phase 2.

These time frames can vary depending on various factors, which is why it’s so important to work with a good practitioner.

It may appear onerous, but by persevering with these therapeutic diets, the results can be really worthwhile to to help you to heal and regain vitality.

While these diets are not technically considered a cure, the idea is to eliminate foods considered detrimental, and include foods that support your body to give it the best chance to heal naturally and regain balance and vitality. That’s why it is so important to exclude antagonistic foods and drinks such as gluten, dairy, additives, and sugar.

Important: Before you commence a new diet, see your medical or health care professional for qualified guidance about what foods and supplements are best for your body. While on the diet do not stop any medications or supplements previously prescribed unless advised otherwise by your medical or health care professional.

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.

Intermittent fasting to heal leaky gut

As mentioned, if symptoms are mild it could be worthwhile to initially trial an Intermittent Fasting Diet for 3 weeks to see if symptoms improve. If not, the next step is a Leaky Gut Diet, or possibly a Leaky Gut/SIBO dietary combination.

Intermittent fasting is more about changing when you eat, rather than not eating. It can be an amazing tool to heal the gut. Apart from healing a leaky gut, intermittent fasting has been reported to have many other benefits, including losing weight, balancing hormones, and even muscle building.

The idea of an intermittent fast is to give your body the time and space it needs to heal without imposing on it with more food at the wrong time. Also, when you eat, your body uses more energy for digestion, which instead could be used to aid the healing process.

There are various types of intermittent fasts, but to heal leaky gut an easy fast is the daily type where you have a 16-18hr window of fasting between your night time meal and break-fast the next day.

For example, you could eat your evening meal at 6pm and your next meal (following a 16 to 18 hour fast) from 10am to noon. Then eat freely until 6pm…and repeat the cycle. If you are hungry outside of these times, the ‘go to’ is clear bone broth or water, as our bodies are often thirsty rather than hungry.

The 16-18hr daily fast time allows your intestinal tract to heal because it is very hard for a gut to heal that is constantly digesting food. That’s because the process of digestion is an inflammatory activity in itself, even without considering the type of food you are eating.

You are still encouraged to eat the same calories/kilojoules in the 6-8hr window you would normally consume so your body doesn’t feel that you are starving it, and you will also get enough of the nutrients your body needs. It’s preferable to have a later break-fast because the morning is when the body naturally goes into detoxification and elimination mode, expelling waste matter through bowel movements.

It’s important to eat healthy foods to help reduce inflammation rather than pro-inflammatory foods. That way your body will naturally produce the hormones needed to maintain good health.

The good thing about an intermittent fasting diet is that it’s healthy and sustainable – a lifestyle diet you may wish to continue, or come back to after healing leaky gut.

Histamine intolerance and leaky gut

Most people who have leaky gut have SIBO, and many people who have SIBO have histamine intolerance.

Even though the foods in a leaky gut healing diet are soothing and gut restorative, for some people who have histamine intolerance, these healing foods (bone broth, pre and probiotics and fermented foods) can actually make them feel a lot worse because of the extra histamines in these foods. Also, if you have an overgrowth of the wrong bacteria in your gut or parasites, these critters actually secrete histamine.

What is histamine?

Histamine is a neurotransmitter (chemical). Its job is to communicate important messages from your body to your brain, increase stomach acid to help you break down food, and assist the immune system to fight invading pathogens. Your body needs just the right amount of histamine to do its jobs, not too much and not too little.

An imbalance of bacteria in the intestines means there are more ‘bad bugs’ than ‘good bugs’. These ‘bad bugs’ are the bacteria and parasites that secrete histamine, which creates inflammation and irritation.

In this inflamed state, the gut may not be able to create enough enzymes needed to deal with the extra histamines, which we see this in leaky gut and SIBO (small intestine bacterial overgrowth).

This can create a cyclic effect of inflammation – the gut creates more histamine and higher histamine creates more inflammation. This is why we initially reduce the amount of added histamines from food in Phase 1 of the Leaky Gut Diet and Phase 1 of the SIBO Diet to allow the gut to settle the inflammation.

After a few weeks or so (determined by your practitioner, based on your symptoms), we introduce gut healing foods that are high in natural histamines. These are beneficial to balance the healing needed to restore the bacterial balance. (using pre and pro-biotic foods)

After a few weeks or so (determined by your practitioner, based on your symptoms) to clear we introduce gut healing foods that are high in natural histamines. These are beneficial to balance the healing needed to restore the bacterial balance, using pre and pro-biotic foods.

Symptoms of a histamine intolerance or overload of histamine in the body

  • Rash or itching (anywhere)
  • Heartburn or acid reflux
  • Headache or migraine
  • Gas, bloating, cramping and diarrhea or constipation
  • Dry or swollen lips
  • Muscle tremors or twitching
  • Anxiety or panic attack
  • Insomnia
  • Low blood pressure, irregular or racing heart beat
  • Asthma, acne or eczema

Histamine and Diet

Histamine is naturally high in some foods, but lower in others. However, time can increase histamine levels. For example, left over foods have more histamine compared to fresh foods.

You may have a threshold level of histamine in foods that you are fine with, but the combo of a bacterial imbalance in your gut and a glass of red wine or piece of chocolate, which are naturally high in histamine, then whammo – you have one of the above symptoms.

You don’t have to have conditions like hay-fever or allergies to have a histamine problem, but you may have what is called histamine intolerance.

Anybody can have histamine intolerance, but you are at higher risk if you eat: a ‘GAPS’ diet; a low-carb/high protein diet; enjoy gourmet foods; or consume fermented foods. Why? Because histamine is found primarily in aged, fermented, cured, cultured and smoked foods.

The best way to avoid histamines is to shun foods high in histamine, choose fresh foods whenever possible, and look for the ‘packed on’ date of meat or fish being sold. ‘FAS’ (frozen-at-sea) may be your best bet. Grass-fed and pastured meats are not necessarily better choices – it depends on how far it travelled and how long it took to get to your store.

Most beef ‘hangs’ for at least two weeks before it is chopped up, packed, wrapped and shipped to the butcher, even if it comes from a local family farm that pasture raised their animals. Therefore, most beef is aged to some extent.

Once histamine develops in a food, there is no getting rid of it. And if bacteria or yeast are still present in the food then histamine levels will continue to rise.

Many of the symptoms of histamine intolerance are similar to ‘leaky gut’, which is another important reason to avoid high histamine foods, until at least some of the symptoms improve.

When going onto Phase 2 of the Leaky Gut Diet be observant if you get any return or exacerbation of symptoms when you introduce foods like bone broth, fermented foods and probiotic foods. Check with your practitioner if you are unsure about any symptoms or when to progress to the next level of the diet.

There is no such thing as a totally ‘histamine-free diet’, but the best way to reduce your levels is to eat low histamine foods and avoid high histamine foods.

High histamine level foods (to avoid):

  • All alcohol and any other fermented, pickled or canned foods/drinks
  • Cheese, especially matured cheeses
  • Smoked meat products – salami, ham, sausages
  • Shellfish, tinned fish and fish that’s not fresh
  • Beans and pulses – chickpeas, soy beans, peanuts, cashews (not so bad if sprouted)
  • All nuts and nut milks but especially walnuts (can be ok for some people in small amounts especially if soaked)
  • Chocolates and other cocoa based products (raw cacao nibs without sugar can be ok in small amounts for some people)
  • Black tea, green tea and coffee
  • Citrus fruits plus kiwifruit, pineapple, plums, papaya, strawberries & tomatoes
  • Wheat and foods containing yeast as they are a catalyst for histamine generation
  • Vinegar and foods with vinegar such as mustard, mayo
  • All fermented foods are high in histamine, but can be tolerated once the ‘leaky gut’ has had a degree of healing. However, initially avoid bone broth, kefir, kombucha, any fermented foods, yoghurts etc.
  • Ready-made packet meals
  • Salty snacks, sweets with preservatives and artificial colorings & additives – benzoate, sulphites, nitrites, glutamates and food dyes

Low histamine level foods (acceptable):

  • Fresh meat, fish and chicken (cooled, frozen or fresh) and egg yolks
  • Fresh fruits – except those listed below in high histamine section
  • Fresh vegetables – except tomatoes & other nightshade veggies
  • Grains – only rice, buckwheat and quinoa
  • Milk substitutes – coconut milk, rice milk but not nut milks
  • Most oils are fine but do check for rancidity
  • Most leafy herbs
  • Herbal teas – but not black or green tea or coffee

Click to find out more about the Low Histamine Diet

Some find a Low FODMAPs Diet also helps to settle histamine reactions to foods.

The SIBO Diet (Phase 1 & 2)

The clearing phase

As mentioned, most people with Leaky Gut also have SIBO. For those who do, it’s first necessary to clear bacterial imbalance and any parasites.

You will need to follow the SIBO Diet for 12 weeks (6 weeks Phase 1 + 6 weeks Phase 2) or longer if necessary, depending on your symptoms. You will need assistance from your integrative/functional doctor or health practitioner as you may need herbs or antibiotics to support this process.

Please go to the SIBO Diet for more information and appropriate foods.

Note: But if you do not have SIBO (and an Intermittent Fasting Diet has not worked for you) then you can bypass the SIBO Diet and go the Diet for Leaky Gut Healing (Phase 1 & 2).

The Leaky Gut Diet (Phase 1)

The Healing and Sealing phase

This phase allows any remaining inflammation to settle, the leaky gut to seal and heal, and for the joins between the cells lining the intestine to become ‘tight junctions’ again. This phase can continue for 1 – 12 weeks, depending on your symptoms and the advice of your health practitioner (and possibly re-testing for leaky gut to confirm sealing).

If the SIBO diet was done to completion, you may not need to be on this phase for long.

This diet is low histamine and avoids grains, legumes, most nuts (except coconut), egg-whites, processed foods, foods with nitrates, sugar, gluten, dairy, additives and nightshade foods.

Enjoy wild-caught fish and pasture fed meat, certain low reactive vegetables and fresh low reactive fruits. Foods are low in histamines, anti-inflammatory and gut healing such as fresh soups, steamed vegetables, healthy fats as well as lots of other yummy foods to bring your body back to harmony. By healing your leaky gut, you can prevent a myriad of health conditions, including auto-immune diseases.

The Leaky Gut Diet (Phase 2)

The Rebuilding and Re-seeding phase

You will need your practitioner or doctor to determine if you require any additional probiotics or herbs and also to ensure you are ready to progress beyond the previous phase.

This last phase slowly reintroduces the fermented foods, probiotic rich foods and bone broths to complete the healing and rejuvenation cycle of gut restoration and to bring balance back to the good bacteria in your digestive system.


step 3.(after completing the Diet for Leaky Gut Healing – Level 1)

Important: Before you commence this diet, see your medical or health care professional for qualified guidance.

After following the Eating4Vitality Level 1 Leaky Gut diet for a period (to be determined by your symptoms and your practitioner’s advice), the food choices will change to focus on the gut restorative foods such as bone broths, fermented foods, pre-and pro-biotic rich foods as well as soups, steamed vegetables, healthy fats (like egg yolks, salmon, avocados and coconut oil) as well as lots of other yummy foods to bring your body back to harmony.

By healing your leaky gut, you can help prevent a myriad of health conditions, including auto-immune diseases.

High histamine foods that are not gut healing are not included in this diet, but you can add these in gradually after your healing program is complete and you and your practitioner are satisfied that you are safe to eat the remaining foods on the high histamine list. Take care by introducing any histamine food gradually to avoid relapsing into previous symptoms.

When you click onto the ‘Leaky Gut (Level 2)’ button you will find a great variety of healthy recipes containing the nutrients to support your body. It’s very simple. But don’t limit your meal choices, because otherwise you may not get all the nutrients you need. And don’t forget to keep evaluating your progress with the Vitality Calculator. You will find it’s invaluable.

Case study: Healing leaky gut and depression naturally

Client name and identifying information changed

When Ronald first came to me he was suffering badly from chronic depression. He had already been on numerous different anti-depressants and even tried electro-convulsive shock therapy (ECT). He had almost given up and at times felt suicidal, but he had much to live for with a loving wife and two small children. His wife initially visited me for her own stress support, and then on her advice, he made an appointment.

He couldn’t remember when it all started or even how, but it seemed to just sneak up on him and gradually get worse to the point where he could no longer work or look after himself. He seemed at a loss.

I said that because he hadn’t responded well to drug treatment, then there must be something else going on that had been previously missed, so I organised a variety of tests. Fortunately, his wife brought along lots of results that had already been screened by his doctors which helped to rule out many possibilities.

I tested him for pyrrole disorder (common in mental health symptoms) but that was all clear. I checked his gut function and it was a mess. He had leaky gut, food allergies and intolerances, no good bacteria at all and a few different types of bad bacteria. Luckily, nothing too harmful but it still undermined his health and gut.

The gut is responsible for about 80% of our serotonin (the happy & relaxing neurotransmitter) so it was obvious that he couldn’t get the right balance of neurotransmitters because of the condition of his gut.

The first thing to do was to remove all offending foods that came up on Ronald’s intolerance test including gluten, dairy, eggs, yeast, most nuts and chocolate (which he constantly ate to try and feel better). I also advised him of the foods that would help to heal and seal his gut.

Fortunately, he had a dedicated wife who could prepare all that he needed. He loved the bone broths and as she said, “he can’t seem to get enough of it, drinking up to 2 litres of the stuff a day”. His body was calling for it.

We also implemented a protocol of herbs to kill off the bad bugs along with some probiotics to re-inoculate the ‘good guys’ as he couldn’t use other fermented foods for a while due to the SIBO (bacterial overgrowth).

Even though he felt much better within a week, it gradually took six months for him to come back to feeling strong enough to go back to work, which he wanted to do. He couldn’t even contemplate working when he first came in.

After twelve months on the diet plus some supplements to speed things up, he was back to his normal chirpy self. I barely recognised him when he came in with his daughter for an infection a few years later. He just looked so vibrant, healthy and happy.


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