Immune system and inflammation
Allergies and intolerances: how the gut learns to tolerate food
Every day the gut has to tolerate foreign protein. How this tolerance develops, what role bacteria, stomach acid and skin play, and why many people feel allergic without being so.
How solid is the research? Trust score 3 of 5:Promising
The basic principles of oral tolerance and the early-introduction strategy are well established. That a disturbed gut flora promotes allergies has been convincingly shown in animals, and in humans through associations. Evidence that an existing allergy can be cured via the gut flora is lacking so far.
Cause or consequence? Root cause 2 of 5:Rather a consequence
Allergies arise when tolerance is not learned or is lost. Best established are inflamed skin in infancy and avoiding allergens; a poorer gut flora, too little stomach acid and too little IgA are considered contributors, shown mostly in animal studies and observations. Activated mast cells are more the tool of an allergy than its cause.
Healthy state
Allergy and intolerance are two different things. In a true food allergy, the immune system reacts to a protein, usually via IgE The antibody of classic allergy. It sits on mast cells and triggers their alarm on contact with the allergen. on Mast cells Immune cells beneath the skin and mucous membranes, filled with histamine and other messengers. They raise the alarm in allergies, infections and stress. More in the chapter “Mast cells: alarm cells in the gut, histamine and the disputed MCAS”. Even small amounts can trigger hives, swelling, breathing difficulties or circulatory shock. In an intolerance, usually an enzyme or a transporter is missing, for example with lactose, and the symptoms depend on the amount.
That we are not allergic to everything we eat is an achievement of the gut. Experts call it Oral tolerance The ability of the immune system to tolerate food protein taken up via the gut as harmless, mediated mainly by regulatory T cells. . Special immune cells in the gut lining take up food protein, carry it to the gut's lymph nodes and present it there to T cells, together with the signal “harmless”. This produces regulatory T cells, which dampen immune reactions against this protein throughout the body. In mice, this pathway needed retinoic acid from vitamin A and the messenger TGF-beta.
Gut bacteria help with this. Mice without Microbiome, gut microbiota The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. More in the chapter “Building microbial diversity” or after antibiotics were more easily sensitised to food protein. One group of bacteria, the clostridia, was protective: they made the gut wall tighter and retuned certain immune cells. When researchers colonised germ-free mice with stool from healthy infants, the animals were protected against cow's milk allergy; with stool from infants with cow's milk allergy, they were not. A single bacterium, Anaerostipes caccae, a Butyrate A short-chain fatty acid and the main energy source for the cells of the colon wall. It strengthens the barrier and dampens inflammation. More in the chapter “Butyrate and other short-chain fatty acids” producer, was enough for part of the protection.
The route by which the immune system first meets a protein also matters. Via the gut, tolerance tends to develop; via inflamed skin, allergy tends to develop. This explains why children with atopic eczema more often develop food allergies, and why avoiding allergens does not protect.
Disrupted state: causes and effects
The best-known proof: in the LEAP study, 640 infants at high risk of allergy were given peanut either regularly or not at all. Among the children without initial sensitisation, at age five 13.7 per cent of the peanut avoiders had an allergy, but only 1.9 per cent of the peanut eaters. Eating early protected, avoiding did harm.
Acid blockers could disturb tolerance. Without stomach acid, proteins are broken down less and arrive in the gut in larger pieces. In 152 adults without known allergy, after three months of acid blockers, 15 per cent formed IgE antibodies against foods in a blood test for the first time; this did not confirm an allergy. In a cohort of almost 800,000 children, infants who were given acid blockers later had a food allergy about twice as often; after antibiotics in the first six months, asthma and hay fever were more common. These are associations; do not stop medically necessary acid blockers on your own because of them.
A gut infection can also trigger a local allergy in the gut. In mice, IgE antibodies against a protein eaten at the same time formed during an infection, only in the gut. Later, this protein caused abdominal pain via mast cells. In people with Irritable bowel syndrome Recurring abdominal pain linked to bowel movements, without tests finding another cause. Today it is understood as a disorder of gut–brain interaction. More in the chapter “The gut-brain axis”, the gut lining swelled after injection of wheat, soy or milk protein. Such a local reaction cannot be seen in a blood test.
At the same time, far more people consider themselves allergic than actually are. In a European Meta-analysis An analysis that combines the results of several studies. It is only as good as the studies it includes. , 6 per cent reported a cow's milk allergy, but it was confirmed by a challenge test in 0.6 per cent. In IBS, 84 per cent of respondents reported symptoms from at least one food, mostly from poorly absorbed carbohydrates such as those in milk, beans or apples.
This matters because wrong diagnoses do harm. If you avoid many foods without reason, you eat a more one-sided diet, lose quality of life and feed your gut bacteria less well. IgG tests for foods only show what you have eaten and are not suitable for diagnosing allergies or intolerances.
Where it comes from and where it leads
The same symptoms can have different roots. This map shows what may be involved in this problem and what may follow from it.
Possible causes. Acid blockers (PPI), Low IgA, Mast cells, First microbiome, Heartburn, Stress & sleep, Low variety, Mould, Hormones & cycle, Long Covid, POTS & connective tissue, Endurance sport, Antibiotics, Medication. Possible consequences. Skin & gut
- Possible causes
- This problem
- Possible consequences
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Move the mouse over a box: its connections are highlighted and everything else steps back.
Tap a box to highlight its connections. Tap it again to open the chapter.
Connections, not certainty: a link means “can”, not “must”. What applies to you is best clarified in a talk with your doctor.
What often helps
Lifestyle
Diet, exercise, sleep, social contact and dealing with stress.
- Offer babies allergens early and regularly The LEAP study showed that early, regular peanut greatly reduces allergies in high-risk children. In children with severe atopic eczema or known egg allergy, introduction should be supervised by a doctor. Recommendations on age differ by country; ask your paediatrician. Established How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [1]
- Treat atopic eczema well Inflamed, cracked skin is a gateway for allergens. According to the skin hypothesis, good skin care and treatment of eczema in infants is one building block of prevention. The evidence is not yet clear-cut. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [2]
Natural supplements
Supplements do not replace a medical check-up. Discuss dosage and interactions with your doctor or pharmacist.
- Probiotics in pregnancy and breastfeeding The World Allergy Organization suggests probiotics for pregnant women, breastfeeding mothers and infants at high risk of allergy, mainly to prevent eczema. The recommendation is conditional and the evidence very uncertain; which strains are best is open. Probiotics do not cure an existing allergy. Plausible How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [3]
Medical treatments
Information, not a treatment recommendation. Decide together with a doctor. Approval and availability differ from country to country.
- Get allergy tested properly The European guideline recommends: first a detailed history, then a skin prick test or specific IgE in the blood, and if needed tests for allergen components. If results are unclear, a medically supervised challenge test is the gold standard. A positive test without matching symptoms does not mean an allergy. Established How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [4]
- No IgG tests for foods Allergy societies explicitly advise against them. IgG against foods is a normal reaction to what you eat, not a sign of an intolerance. Well supported How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [5][6]
- Caution with acid blockers and antibiotics in children In infants, spitting up and crying are very common and mostly harmless. Acid blockers and antibiotics have their place, but should only be given for a clear reason, also because of the possible link with allergies. Promising How we rate the evidence Established Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies. Well supported Several randomised studies in humans with largely consistent results. Promising Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies. Plausible Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms. Experimental Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open. [7][8]
From the community: what people report
Experiences and tips from people with the same problems that come up again and again, but for which there are no meaningful studies yet. They are explicitly not evidence.
Allergy or just intolerance?
In gut forums the question keeps returning whether symptoms after eating come from an allergy or just from an intolerance. Many report that only late, through medical allergy testing, did they learn that bloating, itching or skin rash came from an allergy. Others tell that IgG tests showed them “food allergies” that doctors did not confirm – such IgG tests are not recognised as an allergy test.
Oral allergy and gut flora
Recurringly, those affected describe tingling or reactions in the mouth as well as symptoms after raw fruit and vegetables, which they associate with a pollen allergy (oral allergy syndrome). Some tell that this improved over years with more fibre and a “healthier” gut flora, others that it stayed unchanged. The role of the gut flora is openly described as still not understood.
Histamine intolerance as a consequence of a gut problem
In the histamine community, almost always the same thesis comes up: that the intolerance is only a symptom of a deeper disturbance, such as an overgrowth, an altered gut flora or a leaky barrier. Many report having treated only the histamine symptoms at first and later realised that in doing so they lost sight of the cause. Others report improvement after turning to the gut.
Personal reports can mislead: what helps many people may be a placebo, and what helps one may harm another. Treat them as ideas to raise with your doctor or pharmacist – not as instructions.
In the mood for something completely different? Another one, at random
How we rate the evidence
- Trust score 5 of 5:Established
- Recommended in medical guidelines or supported by several consistent meta-analyses of randomised human studies.
- Trust score 4 of 5:Well supported
- Several randomised studies in humans with largely consistent results.
- Trust score 3 of 5:Promising
- Single randomised or controlled studies in humans, not yet independently confirmed — or many consistent observational studies.
- Trust score 2 of 5:Plausible
- Two cases: first observational or pilot studies with small samples — or a settled basis that is not in dispute, such as movement, sleep or meal pauses. But not tested in humans for symptoms.
- Trust score 1 of 5:Experimental
- Barely studied in humans. Mainly lab and animal studies or theoretical reasoning; whether it helps is open.
Sources
- Du Toit et al. 2015: Early peanut in infants at risk of allergy, LEAP study (New England Journal of Medicine)
- Lack 2008: Risk factors for food allergy and the skin hypothesis (Journal of Allergy and Clinical Immunology)
- Fiocchi et al. 2015: WAO guideline on probiotics for allergy prevention (World Allergy Organization Journal)
- Santos et al. 2023: EAACI guideline on the diagnosis of IgE-mediated food allergy (Allergy)
- EAACI 2008: IgG4 tests for foods are not suitable for diagnosis (Allergy)
- CSACI 2012: Position statement on IgG testing for foods (Allergy, Asthma & Clinical Immunology)
- Untersmayr et al. 2005: Acid blockers promote IgE against foods in adults, 152 people (FASEB Journal)
- Mitre et al. 2018: Acid blockers and antibiotics in infancy and later allergies (JAMA Pediatrics)
- Pabst and Mowat 2012: Oral tolerance to food protein, review (Mucosal Immunology)
- Coombes et al. 2007: Gut immune cells generate regulatory T cells with retinoic acid and TGF-beta (Journal of Experimental Medicine)
- Stefka et al. 2014: Gut bacteria protect against sensitisation to food allergens, mouse study (PNAS)
- Feehley et al. 2019: Gut bacteria from healthy infants protect against food allergy, mouse study (Nature Medicine)
- Aguilera-Lizarraga et al. 2021: Local immune response to food protein causes abdominal pain (Nature)
- Nwaru et al. 2014: Prevalence of food allergies in Europe, meta-analysis (Allergy)
- Böhn et al. 2013: Self-reported food-related symptoms in IBS, 197 people (American Journal of Gastroenterology)
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