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Microbiome, Gut Health And Allergies, And Why There’s No Gut Allergy

Microbiome, Gut Health And Allergies, And Why There’s No Gut Allergy

Allergies and gut health are connected. However, allergies aren't intolerances. Find out the difference and why gut bacteria might treat allergies in the future.

What do milk, eggs, nuts, wheat, soy, fish, and shellfish have in common? That’s right, they cause allergies - in fact, these are the most common triggers of food allergy in the population, responsible for 90% of reactions.

These allergens cause symptoms such as sneezing, a runny or blocked nose, red and watery eyes, hives, swelling, tummy pain, nausea, and diarrhoea. In severe cases, the body can go into an extreme reaction known as anaphylactic shock, a medical emergency that requires immediate attention.

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However, not all allergens are food - some can be inhaled. Pollen, mold, dust mites, pet dander, or even cockroach faeces can trigger allergic asthma or rhinitis. Hayfever is allergic rhinitis that is triggered by pollen, especially in spring.

Allergic asthma is the most common type of asthma. It causes sufferers to feel like they are short of breath, wheezing, coughing, and feeling a tightening sensation in their chest. The overreaction of the immune system causes the airways to tighten and flood with thick mucus, which makes breathing difficult.

What’s the difference between allergy and intolerance?

Allergies and intolerances are actually different medical problems because they are caused by different pathways in the body’s processes. Intolerances take longer to manifest, whereas allergies cause a rapid reaction that can sometimes be deadly.


An allergy is characterised by an overall, systemic immune reaction against a foreign invader, wherein the body’s disease-fighting immune cells misidentify harmless substances as a dangerous bacteria or virus.

Does grass cause allergies and gut health problems by Chang Qing.
Grass can cause seasonal allergies and gut health disturbances

These immune cells then ‘attack’ the allergen, trying to clear it from the body. They produce chemicals called IgE antibodies that bind to the allergen, causing the release of histamine, which is responsible for many of the symptoms of allergy. The symptoms of an allergy are:

  • sneezing
  • runny/stuffy nose
  • red, watery eyes
  • swelling
  • abdominal pain
  • nausea
  • diarrhoea

While allergic symptoms often appear immediately, symptoms of intolerance can take up to 20 hours to manifest as food slowly moves through the digestive system. And, unlike allergy, intolerance never causes anaphylactic shock.

☝️Can seasonal allergies cause stomach problems?☝️ Nausea and diarrhoea are digestive symptoms of allergies, but have other causes too.

Lactose, alcohol, and gluten intolerance

A food intolerance, on the other hand, is when the body can’t digest the food properly, leading to digestive symptoms like bloating, cramps, constipation, or diarrhoea. In some cases, they can cause severe reactions that require immediate medical treatment.

Lactose and alcohol intolerance

Lactose intolerance, for instance, is common in up to three-quarters of East Asians. It is caused by decreased production of a protein, lactase, that breaks down a sugar in milk known as lactose. Almost all infants can digest milk, but this protein ceases to be produced in many people once we age past childhood.

East Asians also commonly experience alcohol intolerance, with a characteristic ‘red flush’ and stuffy nose after drinking alcohol. The red colour comes from the accumulation of acetaldehyde, a toxic breakdown product of alcohol because of decreased production of a protein that breaks acetaldehyde down to a less toxic substance.

Gluten sensitivity and coeliac disease

Issues digesting gluten are triggered by exposure to many grains, such as wheat, barley, and couscous. Coeliac disease is a severe form of intolerance which requires the affected person to cut out all foods containing gluten, which includes very common foods such as bread, cereal, and pasta. It is different to non-celiac gluten sensitivity, a milder health problem that may affect 5% of people.

The difference between allergy and intolerance by Allergyscope

Celiac disease sufferers experience autoimmune inflammation in the small intestine that is triggered by gluten, wherein the immune system attacks the body itself, which if left untreated can lead to conditions that affect other systems of the body, such as infertility, osteoporosis (brittle bones), and chronic fatigue.

Interestingly, 30% of the Caucasian and Western European population carries a gene that predisposes towards celiac disease, but only a small percentage of those with the genes develop celiac disease. The Atlas DNA Test searches for genetic predispositions towards lactose, alcohol, and gluten intolerance.

Gut health and allergies are connected

An allergy can be diagnosed and treated with medication prescribed by a doctor, but there are ways to prevent our risk of developing allergies, starting with a healthy gut. The gut microbiome consists of bacteria that live in our gut in a mutually beneficial relationship with us - they feed us and we feed them.

New research is increasingly finding evidence that a healthy and diverse gut microbiome is associated with fewer allergic symptoms. The rates of allergies have been rising steeply in the last few decades as humans settle in comfortably in urban environments.

Indeed, eating habits have become more homogenised with less variety of food sources. People get outdoors less and do less exercise. Families are also having fewer children and taking more antibiotics. In particular, antibiotics are a potent disruptor of microbial balance in the human gut.

Gluten gut allergy by Maddi Bazzocco.
Gluten causes intolerance but nuts cause allergies

All these factors cause our microbiomes to lose precious diversity, decreasing the number of species in the ‘database’ that our immune system can recognise as foreign, yet not overreact, because it knows that they are not harmful.

In fact, this idea is not new. As far back as 1989, the hygiene hypothesis of allergy was proposed, stating that the greater our exposure to microorganisms, the lower our risk of developing allergies. This doesn’t refer to how often you tidy your room or wash your hands, but rather to factors that affect your level of exposure to microorganisms.

This was because ancient humans, during the evolution of our relationship with microorganisms, derived lots of benefits from a symbiotic relationship with species that existed in the same environments as human hunter-gatherer and farming communities, surrounded by mud and vegetation.

This includes microorganisms living on other people in the community, which we grew accustomed to, and those that infected us at low levels we could tolerate and learn to build immune defenses against. Fortunately, there are some simple things that can increase your exposure to microbes:

Having one or more older siblings
Living in a rural rather than urban area
Owning a pet

These microbes have persisted in our guts, forming an integral part of our immune system’s control against foreign agents. Hence, modern environments, which compromise their existence, have a knock-on effect of compromising our immune system, which overreacts to allergens as if they were these ancient microbes, kicking our bodies into defense mode.

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Microbiome diversity develops from birth

Microbiome diversity develops the most between the ages of 0-3, continues development throughout childhood, and stabilises in adulthood.

As soon as a baby is born, microorganisms from the environment begin colonising their microbiome. In fact, vaginal delivery has been shown to increase microbiome diversity in babies compared to delivery by Caesarean section, providing protection against allergies later in life.

Breastmilk for gut allergy by Valeria Zoncoll.
Breastmilk contains essential pre and probiotics

Breastfeeding also directly transmits beneficial bacteria such as Lactobacilli and Bifidobacteria to the infant, and it is rich in sugars known as oligosaccharides that nourish these microbes,, which in turn feedback to the developing infant immune system via molecular signals.

While often unavoidable due to infections, the use of antibiotics during pregnancy and infancy has been linked to increased risk of allergies later in life.

Probiotic and food allergies

The good news about allergies is that children sometimes outgrow them. Three-quarters of children with milk or egg allergies outgrow it by age 16, and 20% of children with peanut allergy do outgrow it. Nevertheless, there is plenty parents can do for themselves and their kids to lower the risk of developing allergies in the first place.

Researchers in Boston have recently identified the species of gut bacteria, Clostridiales and Bacteroidetes, that protects against the development of food allergies in children. When these microbes were given to mice, it increased the mice’s tolerance to food allergens and reversed their pre-existing food allergies.

The scientists speculated that in future, giving such bacteria to children whose microbiomes show signs of forming allergies could help prevent these allergies from forming in the first place. Flagging such infants is already being done - in one study, three-month olds who were found to lack four key microbe groups were more likely to develop asthma by age three.

☝️FACT☝️There is no best probiotic for food allergies, but in the future, it may be a possibility thanks to microbiome technology and ongoing research.

Is there a link between probiotics and food allergies?

Prevention, after all, is better than a cure. Current methods aim to develop an individual’s tolerance by feeding them slowly increasing amounts of food allergens, but this is time consuming, requiring the person to commit to a long course of consistent exposure to the allergen - not to mention the risk of side effects.

Improve allergies and gut health with plant foods by Ella Olsson.
Prebiotic plant foods are sustenance for probiotic microbes

Probiotics are live beneficial bacteria we can intake orally, and prebiotics are substances that directly feed the gut bacteria. Both have been shown to increase gut health. An example of prebiotics is fibre, which nourishes bacteria in our gut that produce butyrate, allowing them to keep the gut lining healthy and maintain a balanced symbiotic community.

There is early evidence that synbiotics, which are a combination of pre and probiotics, protect the microbiomes of infants predisposed towards cow’s milk allergy. Even if a child already has an allergy, probiotics can help, with experiments showing that they increased the effectiveness of oral immunotherapy in a cohort of 62 children with peanut allergies.

☝️FACT☝️Some people may be sensitive to probiotics, particularly if they have a very weak immune system. However, these reactions aren’t probiotic food allergies.

How to alleviate seasonal allergies and digestive problems

Supplying oral probiotics in adults with rhinitis - the stuffy nose that is often caused by seasonal allergies - was also shown to help, with Lactococcus lactis protecting against bacteria that cause pneumonia (a severe lung infection) by increasing the rate of clearance of these pathogenic microbes from the lungs.

A balanced, diverse diet with lots of fibre and oligosaccharides supplied during pregnancy may help protect against later allergy development in babies. Whole grains, beans, vegetables, fruit, nuts, and seeds are all sources of fibre, including prebiotic fibers that also benefit the gut microbiome.

Last but not least, exercise, perhaps the simplest and least complex intervention, has been proven to increase microbiome diversity. In mouse models, this diet increased amounts of beneficial bacteria, Lactobacillus and Clostridium leptum, that protect against wheat allergy. Regular exercise also is linked to greater gut microbial diversity, yet another excellent reason to make physical activity part of your life.

The final word: is it a gut allergy?

So after all, there may be more to allergies than meets the eye - and more we can do about it than we previously thought possible. While gut bacteria and allergies continue to be an active area of research, careful nutrition and diet, along with early interventions, could help children be free of allergies for life.

However, even though there is a connection between gut health and allergies, there is no gut allergy. Rather, the gut can help mediate the body’s reaction to an allergen. That said, food intolerances to gluten and lactose directly affect the gut, but they have different symptoms.

Shu En Lee
Shu En Lee Biotech enthusiast who loves the cutting edge of science

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