Nutritional protocols for gut permeability

Terms used for gut permeability

Beautiful Woman With Stomach Illustration.

A ‘leaky gut’ is simply a term used for a permeable gut lining associated with inflammation; where nutrition practitioners may use the term ‘leaky gut’, gastroenterologists will use the long-winded term ‘gastrointestinal hyper permeability’.

Various terms are used to describe gut permeability. Controversy exists with the commonly used term leaky gut syndrome, as some practitioners have blown it out of proportion, suggesting it to be a disease. In reality, it is evident that a ‘leaky gut’ is simply a term used for a permeable gut lining associated with inflammation. Nutrition practitioners more frequently use the term ‘leaky gut’ whereas gastroenterologists may use the long-winded term ‘gastrointestinal hyper permeability’.

What is a leaky gut?

In a healthy digestive tract, the cells lining the intestines are plumped up and closely packed together, carefully controlling the absorption of nutrients from food. In an individual with a leaky gut (a semi-permeable gut lining), the cells become inflamed and gaps appear between the cells, with damage to the tight junctions large enough for food particles and other toxins to enter directly into the bloodstream. Damage to villi may also occur, leading to malabsorption. If someone’s digestion is in a poor condition, undigested food particles may pass through these gaps between the cells in the intestines, and the immune system may react to this by creating more inflammation, i.e. an intolerance. Excess inflammation can cause further damage to cells, exacerbating the problem. A leaky gut is therefore often an ongoing inflammatory issue, and frequently remains undiagnosed.

Key roles of the gut impacting other health factors

A permeable gut lining does not only present as digestive symptoms, as it can also have a knock-on effect on many other processes in the body, which can result in other symptoms. A leaky gut significantly affects absorption of vitamins and minerals; as a result, therefore, a low nutritional status in the body may reduce production of bile and digestive enzymes, further impacting absorption of nutrients.

Immune function also relies on the integrity of the digestive system, as approximately 70% of our immune function is dependent on the beneficial bacteria present. If the gut is compromised and pathogenic bacteria are abundant, the body’s efficiency in fighting off infections is reduced. This may contribute to autoimmune conditions such as rheumatoid arthritis.

Regulation of hormones is also dependent on digestion, due to possible reabsorption of hormones in the large intestine. Intestinal function affects stool transit time, therefore a permeable gut lining may alter hormone levels, impacting mood and skin health in particular.

Food intolerances as a result of a leaky gut can also result in many non-digestive symptoms, as the immune (usually an IgG) reaction can cause a response such as sinusitis and fatigue. Fatigue is a common side effect of a leaky gut, and another contributing factor may be due to a reduced production of the intrinsic factor in the stomach which supports vitamin B12 absorption in the intestines. As a result of low intrinsic factor production, this may lead to a B12 deficiency, possibly leading to anaemia.


Although clients may not have noticed or considered an association between their symptoms, such as fatigue, and their digestive issues, they are of course very much interlinked.

The most common symptoms you would expect from a leaky gut include digestive complaints such as diarrhoea, constipation or a combination of the two. Bloating, cramping and excess wind may also occur. Most importantly, common to a damaged digestive tract is often a ‘burning’ sensation in the stomach or small intestines following a spicy meal, or after drinking alcohol.

Other non-digestive symptoms may include mood swings, headaches, depression, anxiety, skin acne, dry itchy skin, fatigue and joint pain.

Health issues linked to gut permeability

Several conditions may independently increase gut permeability, therefore if a client has one of these conditions, you may wish to consider their gut health and follow a gut-healing protocol. Inflammatory bowel diseases such as ulcerative colitis and Crohn’s disease involve a significant level of permeable gut lining, including ulcers. Although the cause may not always be understood, it is evident that the gut will have considerable damage in this case. Other conditions such as HIV / AIDS, type 1 diabetes and coeliac disease will also involve a compromised gut lining due to immune suppression or over-activity, inflammation and reduced circulation.

The cause of a leaky gut

There is no one simple cause of a leaky gut; a combination of chronic inflammation, nutritional deficiencies, improper digestion and high intake of commonly aggravating foods and stress are usually to blame. Other possible causes of a permeable gut lining can include parasites and bacterial or yeast infections. An invasion of such pathogens can easily result in inflamed and irritated cells lining the gut, which can then lead to a leaky gut and also an increased level of toxins which may be released from the pathogens.


Inflammation plays a key role in the development of a leaky gut. Although inflammation is the body’s natural response to an injury or infection in order to promote healing, long-term inflammation causes a simultaneous breakdown of tissues, leading to damage. Excess damage to tissues may lead to damage in tight junctions usually holding mucosal cells together and resulting intolerances due to a leaky gut may further exacerbate the problem by causing yet further inflammation. This constant high level of inflammation makes it very difficult for the body to heal itself.

Chronic inflammation may be a result of an inflammatory diet, consisting of foods high in refined carbohydrates, in particular from grains such as white bread, and also a diet high in the omega-6 fatty acid arachidonic acid (AA). Omega-6 AA is found in grain-fed meats; a diet consisting of cheaply produced meat and processed foods is therefore most likely to either contribute to or exacerbate symptoms of a leaky gut.

Nutritional deficiencies

Deficiencies of important nutrients including zinc, antioxidants, protein and fatty acids may be another possible cause of a leaky gut. Zinc is essential for cell growth and replication, antioxidants are required to protect cells against oxidative damage and protein is required for cell integrity.

Fatty acids are particularly important, for numerous reasons, including keeping cell membranes fluid enough to optimise transport of nutrients and toxins. As fatty acids have such an impact on inflammation in the body, this is another reason a fatty acid deficiency may cause damage to a gut lining. A deficiency of omega-3 EPA would lead to an increase in inflammation due to a high omega-6 to omega-3 ratio.

Improper digestion

Inadequate production of digestive juices may lead to improper digestion of food particles which may increase risk of food intolerances. A sufficient amount of stomach acid, bile and digestive enzymes are required to support optimum digestion and therefore to avoid problems associated with a leaky gut.


There are several foods which may worsen the symptoms of a leaky gut by directly aggravating the mucosal cells.

Gluten, found in wheat, barley and rye can be particularly difficult to process in the body for some individuals, and it can result in immune reactions leading to unwanted symptoms such as digestive cramps. Gluten is one of the most common food intolerances and can negatively affect symptoms of a leaky gut.

Gluten is also inflammatory, so long-term intake of high gluten-containing foods may also contribute to the development of a leaky gut, especially for those who experience symptoms after eating such foods. If someone is having toast or cereal for breakfast followed by a sandwich for lunch, and pasta for dinner, their intake of gluten will be very high.

Spicy food

Chilli peppers contain a compound called capsaicin, which, as you may have noticed, causes irritation to mucosal cells, including the lips, tongue, mouth and digestive tract. With a healthy digestive lining, it is possible to withstand a certain amount of spicy food without symptoms. Everyone has their own critical point as to how much spicy food they can withstand, but if you imagine the inflamed cells in a leaky gut, the sensitivity is high, therefore even a small amount of spicy food can result in a burning sensation in the stomach and a bout of diarrhoea. Diarrhoea is the body’s way of flushing out something that is causing harm; therefore, if someone experiences diarrhoea the morning after a spicy curry, they are very likely to have a permeable gut lining.

Ginger and other strong foods

Certain foods, such as ginger, garlic and onions, are very pungent. Although these foods are considered to be anti-inflammatory, they can also cause irritation to the gut lining if it is already semi-permeable. This is particularly the case for someone with inflammation of the stomach lining (gastritis). Direct contact of such strong foods on already damaged cells can result in an instant burning sensation in the stomach or small intestine.


Stress can have a direct impact on digestive function by reducing stomach acid in mild stress and possibly increasing production over long periods of chronic stress, which may result in either undigested food particles or gastritis, potentially leading, in severe cases, to ulcers. Stress may also reduce production of digestive enzymes as this is not the body’s priority during a stressful episode. Chronic stress may also increase need for antioxidants and may result in high cortisol production which may increase damage to mucosal cells.


Yeast infections such as candida albicans and parasite or bacterial infections may also cause a permeable gut lining by causing direct aggravation, by causing inflammation and by affecting ability to absorb nutrients.


Drinking alcohol in excess, i.e. more than approximately 4 units in one day, can cause significant irritation to an already permeable gut. Alcohol is inflammatory, and therefore is only going to make the situation worse. 2-3 units of alcohol may not cause any issue to someone with a healthy gut lining, but for someone with a permeable gut lining, alcohol can be very aggravating.


There are several medications which are well known irritants, including aspirin, the birth control pill and non-steroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen. These medications may cause inflammation in a particular area of the bowel, which may result in a permeable gut lining or possibly ulcers. Antibiotics may also have a negative effect by wiping out all beneficial bacteria, leaving the gut more prone to infections.


The first step in diagnosing a leaky gut is to identify as many symptoms as possible. You can usually diagnose through symptoms related to intolerances including bloating and stomach cramps after eating, or a feeling of ‘sensitivity’ to certain foods such as bread. If your client has an intolerance to a food, or several foods, they almost certainly have a leaky gut. Symptoms of a food intolerance can range from the understandable digestive complaints of bloating and diarrhoea, to sinusitis, eczema, migraines, joint pains and chronic fatigue.

In addition to identifying a leaky gut through symptoms, it is ideal to carry out a digestive stool analysis. This can give greater understanding of digestive ability, any pathogens which may be present, and also the likelihood of any intolerance. A digestive stool analysis can reveal this information by testing secretory IgA (Immunoglobulin A) levels. IgA is an antibody used by the immune system to identify and fight off unwanted objects such as infectious bacteria, and this specific type of antibody is produced in mucosal linings (the gut wall). As unwanted undigested food particles may pass through the gut lining, the immune reaction involving high levels of IgA antibodies may suggest a permeable gut lining.

Protocol: step 1 – eliminate irritating foods

First you need to identify any irritating foods and eliminate these from the diet. Gluten is the most common culprit, although many other foods – such as peanuts, beans and lentils – can also cause problems in some individuals. A food intolerance test may be useful for identifying which foods the body is reacting to. Offending foods only have to be eliminated from the diet temporarily while concentrating on healing the gut. If someone has a leaky gut, they are likely to develop intolerances to several foods, so simply cutting out these foods will not address the cause. Once the gut is properly healed, these intolerances should disappear, as the undigested food particles should not be able to pass through directly into the bloodstream where the immune system could react.

Alcohol and spicy food should also be eliminated (or at least significantly reduced) during this initial stage of approximately 2 months, giving the cells on the gut lining a chance to recover properly. Drinking alcohol even once a week while trying to heal the gut can make the healing process twice as long, so if your client can eliminate it completely for 2 months, this should give their body a helping hand in speeding up their gut recovery.

Protocol: step 2 – test and eliminate pathogens

If a digestive stool analysis identifies an infection such as a bacterial imbalance, probiotics or other supplements specific to eliminating other types of pathogens may be required. It may be possible to treat mild bacterial imbalances and yeast infections with probiotics and supplements specific to eliminating pathogenic bacteria, such as oregano oil and garlic capsules (garlic supplements are less aggravating to the gut lining compared to raw garlic). If a bacterial infection such as H. Pylori exists, your client may require medical attention from a doctor and medication.

Some parasites may also be destroyed with supplementation over several months including use of goldenseal and oregano oil, but as above, the more persistent parasites may require medical attention.

During this stage, ensure that the liver and immune system are supported well with a good intake of antioxidants and the Brassica group of vegetables, protein and omega-3 fatty acids.

Protocol: step 3 – feed your cells

After all aggravating foods have been eliminated from your diet, and pathogens have been identified and eliminated, it is important to concentrate on feeding the cells lining your digestive system and to keep inflammation down in order to promote healing. Cells lining the digestive tract require the amino acid glutamine to be able to replenish themselves, so ensure you take a supplement containing glutamine. The powder form mixed with water is ideal, to maximise exposure to cells if your digestive system is not strong enough to break down supplement tablets.

Protocol: step 4 – control inflammation

Pharmepa TG EPA 90 Step 1 3D side view - cropped - Copy (2)

Reducing inflammation is a key step in eliminating a leaky gut; anti-inflammatory supplements such as omega-3 EPA, aloe vera and liquorice may help to calm and soothe the gut lining.

To control inflammation, consider anti-inflammatory foods like vegetables and oily fish, which are rich in antioxidants and omega-3 EPA fats. Anti-inflammatory supplements which may help to calm and soothe the gut lining include omega-3 EPA, aloe vera and liquorice. Ideally you need 1000mg omega-3 EPA per day to have a therapeutic effect on reducing inflammation, such as Igennus Pharmepa: Step 1, derived from sustainable wild anchovies. For vegetarians, consider echium seed oil, rich in omega-3 stearidonic acid (SDA), the precursor to omega-3 EPA. Slippery elm and marshmallow root are also great soothing supplements with mucous-like properties.

Long-term support

After following a 2-4 month gut healing protocol, your client should be able to slowly introduce foods again. To prevent a recurring leaky gut, keep inflammation at a controlled low level through diet and supplements, and recommend limiting consumption of foods or drinks that cause irritation.

Further advice given to clients in the long term could include optimisation of digestion through supplementation of digestive enzymes, HCL (hydrochloric acid) and probiotics. Digestive enzymes and HCL should only be recommended for someone with a healthy gut lining, therefore should only be considered once the gut is healed.

Stress management, regular exercise, good habits such as chewing food properly and eating while resting, not on-the-go, should also be considered in the long term prevention of leaky gut reoccurring.


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Kyla Newcombe

About Kyla Newcombe

Kyla is a highly qualified clinical nutritionist with a master’s degree in Nutritional Medicine. Kyla runs her own private practice, offering personalised dietary and supplement advice. Kyla has extensive experience in weight management, skin disorders and digestive issues. Her website is at Kyla regularly contributes to articles for leading consumer magazines, and blogs about healthy cake ingredients and recipes at