Food Intolerances: Symptoms, Causes & Diagnosis

 by Liesa Huppertz
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Food allergies, food intolerances, food sensitivities - When it comes to the reaction of our body towards food, there is a lot to watch out for.

Physical reaction to certain foods are common, but mostly they are not caused by a food allergy but rather a food intolerance. A lot of the time, people mix up those two even though the differences are critical.

That’s why in this blog post we are going to talk about the differences between food intolerances and food allergies, about the role of the gastrointestinal tract in food intolerances, about symptomes and finally about the importance of an elimination diet.

Food Intolerances vs. Food Allergy.

Food intolerance is also known as non-lgE mediated food hypersensitivity or non-allergic food hypersensitivity. A food intolerance refers to the difficulty in digesting certain foods and it is different from food allergies in that an allergy triggers the immune system, while food intolerance does not. Still some of the symptoms of a food allergy may be similar to those of a food intolerance.

When having a food allergy, your immune system mistakenly treats proteins found in food as a threat and reacts by releasing massive amounts of chemicals, including histamine. That triggers a cascade of typical allergy symptoms such as a rash or itching after eating just a small amount of a certain food. In some cases, allergies can even be life-threatening as they can cause anaphylaxis which can affect several areas of the body, including breathing and blood circulation.

Food intolerances and sensitivities on the other hand, aren’t life-threatening, just very unpleasant. They are extremely common and seem to be on the rise (1).

In fact, research suggests that more than 20% of the population in industrialized countries suffer from food intolerance or food allergy (2).

Foods most commonly associated with food intolerance include wheat, milk, soy, peanuts, tree nuts, shellfish, eggs and fish.

Food intolerances and sensitivities have a wide range of symptoms, sometimes even similar to food allergy symptoms, making it hard for us to diagnose them.

Food Intolerance: Symptoms.

Certain foods, even the healthy ones can cause bad reactions in the body. Symptoms of food intolerances vary, but most often they involve the digestive system, skin and respiratory system.

food intolerance symptoms

Common food intolerance symptoms include:

  • Diarrhea
  • Bloating
  • Constipation
  • Flatulence
  • Nausea
  • Abdominal pain
  • Rashes
  • Hives
  • Swelling
  • Acne
  • Flushing of the skin
  • Eczema
  • Itchy skin
  • Headaches
  • Migraines
  • Runny nose
  • Fatigue & tiredness
  • Reflux

These symptoms are an effect of a reaction of our gastrointestinal tract to a particular food. When a particular food upsets our G.I. tract, or negatively reacts with one of its constituents, we can feel the effect all over our body.

Food Intolerances: Causes.

It’s very hard to pinpoint a food intolerance to one specific cause as there are many causes of food intolerance. Let’s take a look at some of them.

Lack Of An Enzyme

In order to digest a food fully, your body needs enzymes. Sometimes however, your body is missing certain digestive enzymes, thus food molecules cannot be digested properly.

This is the case e.g. for people who are lactose intolerant. They are missing the enzyme lactase, the enzyme that breaks down milk sugar into smaller molecules which the body can further break down and absorb through the intestine. Remaining lactase in the digestive tract can cause bloating, diarrhea, stomachache, and gas. 4

For proper digestion nearly all foods require an enzyme. According to the British Allergy Foundation, a common cause of food intolerance is in fact enzyme deficiencies.

Transport Defects

Apart from enzyme deficiencies, there may also be defects in transporter molecules. GLUT 5 for example transports fructose, GLUT 2 transports glucose, galactose or fructose. When they don’t function properly, these carbohydrates can’t be transported into the intestinal cells which results in their metabolism in the large intestines where they are transported intact in large quantities. As a result from these gases and decomposition products abdominal pain, bloating, flatulence, and diarrhea may occur.

Chemicals In Foods

Our food is full of chemicals. Take for example caffeine in coffee, tea, and chocolate, or amines in certain cheeses. Some people react harder on these chemicals than others.

Histamine In Foods

Your body naturally produces histamine along with the enzyme diamine oxidase (DAO). Also certain types of food can have an accumulation of histamine. Some people are particularly sensitive to this naturally-occurring histamine. They react with skin rashes, abdominal cramps, nausea, vomiting, and diarrhea.

Most common food intolerances.

According to estimations, more than 20% of the world’s population have a food intolerance. There seem to be certain groups of food that are more common to trigger a reaction in the body than others.

The eight most common groups of food intolerances are:

  1. Dairy
  2. Gluten
  3. Caffeine
  4. Salicylates (natural chemicals produced by plants)
  5. Amines (produced by bacteria during fermentation)
  6. FODMAPs (fermentable oligo-, di-, monosaccharides and polyols)
  7. Sulfites (chemicals used as preservatives in food)
  8. Fructose

Gut Health And Food Sensitivities.

Our gut digests everything we consume. So it’s only natural that the key place of interest when it comes to food sensitivities, allergies and intolerances is in the gut and the gastrointestinal tract. The G.I. tract is a massively important organ system. It’s where nutrients and water from foods are absorbed to help keeping your body healthy. It’s also home to up to 80% of our immune system. Thus gut health is the core of our total well-being.

Leaky Gut And Food Sensitivities.

The role of your G.I. tract is to take in the food you eat, break it down and have it absorbed into your body in a controlled way. Your gastrointestinal system discharges the proper amount of enzymes and acids to process the food so that nutrients can be released and transported to the cells - that is if it is healthy.

Your G.I. tract also provides a protective barrier between the food you eat and the inside of your body. It’s only one very thin layer of cells that separates our digestive system from our bloodstream. When everything is healthy and functioning efficiently, only specific food molecules in specific places and at specific times can enter. When it’s compromised in any way, it may let in food molecules that are not properly digested. (3) This triggers the immune system, which tries to remove these substances: after all, that’s not a place for them to be. This triggers an inflammatory response throughout the body which can cause a wide range of different unpleasant symptoms all over your body.

Furthermore, this can also trigger reactions to usually harmless foods due to high inflammation levels and confused immune cells. This may contribute to food allergies and sensitivities. Here the vicious circle begins as food sensitivities further drive inflammation levels and inflame the intestinal lining which exacerbates leaky gut. Can you see why a healthy gut is so important?

The Connection Between The Gut Flora And Food Allergies.

The key to a healthy gut is bacteria. Our digestive system is host to over 100 trillion bacteria cells. These beneficial bacteria are known as probiotics and they aid in the nourishment and defense of the digestive tract and the whole body. They also help maintain a healthy microbial balance in the digestive system.

Probiotics are also essential for the synthesization of B vitamins and vitamin K, and they produce digestive enzymes to help with the absorption of nutrients.

Unfortunately, our often unhealthy lifestyle consisting of stress, medications, environmental toxins and a diet filled with refined foods and preservatives, can lead to a depletion of these naturally occurring bacteria.

The delicate balance in the gut gets upset by this depletion in friendly bacteria which can allow for some not too friendly bacteria, yeasts, parasites and other various microbes to flourish. This leads to an imbalance in the gut flora which can impair immune tolerance, resulting in food intolerances. (4)

Several studies have shown the connection between our gut flora and the development of food allergies. Most of these studies have been conducted in infants and children, showing that a decrease in Lactobacilli and an increase in Staphylococcus aureus can be linked to egg and milk allergies (5). Also, certain species of bacteria are responsible for the breakdown of gluten protein. A lack of these may result in a gluten intolerance (6). An overgrowth of bacteria that produce histamine or that make enzymes that interfere with the metabolism of histamine is linked to histamine intolerance (7, 8).

So you see that your gut microbiome plays an important role in how your immune system reacts to threats like bacteria or viruses, but what’s even more important here is that you also see that a lack of beneficial bacteria in the gut can in fact contribute to the immune system’s inability to tell friend from foe. This leads to the dreaded overreaction that you experience as an allergy.


Apart from food allergies, there are also FODMAPs. FODMAP stands for “fermentable oligo-, di-, mono-saccharides and polyols”.

These are short-chain carbohydrates which are resistant to digestion.

FODMAPs are naturally present in food an the human diet and can cause digestive discomfort in some people. That’s because they are not absorbed into the bloodstream but reach the far end of the intestine where your gut bacteria then use these carbs for fuel, producing hydrogen gas, which may cause digestive symptoms.

FODMAPs may also cause diarrhea as they draw liquid into your intestine.

Commonly used FODMAPs comprise of:

  • Fructose: Also referred to as fruit sugar as it is a simple sugar found in many fruits.
  • Lactose: A carbohydrate found in dairy products.
  • Polyols: Sugar alcohols including sorbitol, xylitol, and mannitol.
  • Fructans: A polymer of fructose molecules, found in many foods including grains like wheat, rye, and spelt.
  • Galactans: A type of oligosaccharide (a complex carb) found in legumes.

Why Is It Important To Identify And Neutralize Food Sensitivities?

Many symptoms of a food sensitivity reaction only bother us for a short while, but there may be long term consequencesof repeat reactions. Thus, if left untreated, allergies and food sensitivities can have a serious impact on your quality of life. Consequences vary from increased risk of health problems to decreased brain function and mood instability. There even is a risk of chronic diseases (9) and illnesses such as (10):

  • Anaemia

Auto-immune conditions like:

  • Rheumatoid arthritis
  • Diabetes Type I
  • Graves’ disease
  • Crohn’s Disease and others
  • Bowel cancer
  • Depression
  • Infertility
  • Malnutrition
  • Celiac Disease
  • Diabetes Type II
  • and more

Due to the inflammatory effects of allergic reactions, the structure of the system it affects (usually the skin, airway, or gastrointestinal tract) may change. Structural changes e.g. in the airway can lead to asthma or chronic ear and sinus infection while changes to the skin lead to eczema 2. (11)

Save your health and quality of life by seeking professional advice early if you suspect having a food intolerance.

Food Intolerance: Diagnosis.

As you may know by now, not all reactions to food are of allergic nature. In a food allergy, your immune system produces antibodies known as immunoglobulin E (IgE) in response to certain foods that it mistakenly believes to be harmful. This results in a cascade of cellular responses, such as the release of histamines that cause typical allergy symptoms.

Sometimes IgE has nothing to do with a reaction you experience after eating a particular food. What you are experiencing may be a food intolerance which can cause similar reactions to an allergy.

We have already talked about the causes of food intolerances (lack of an enzyme, sensitivity to certain chemicals, histamines in food,...). These different causes make it tricky to diagnose a food intolerance as your doctor or allergist may need to perform a variety of investigations to pinpoint the cause.

There are different tools people commonly employ to identify the cause of a food intolerance. They range from Endoscopy ( a non-surgical examination that is used to diagnose celiac disease) to simple blood tests and hydrogen breath test (a diagnostic tool that is used to detect bacterial overgrowth in the intestines as well as malabsorption of carbs such as fructose or lactose), to keeping a food diary or an elimination diet.

Let’s take a closer look at the ladder.

Elimination Diet to Diagnose Food Intolerances.

The elimination diet is a great tool to uncover hidden food intolerances, healing the gut, and bringing inflammation levels down.

It works by removing the foods that are most likely to irritate your body for a few weeks (three weeks are seen as the minimum) and up to six months to give your body a chance to calm down and focus on healing.

After a three weeks to six months you can bring those foods back one by one in order to identify what specifically is hurting your body. Try to eat the specific food every day for at least one week before you reintroduce the next one.

There are several different ways of doing an elimination diet, starting from the length of eliminating the food to which food you actually do eliminate. Let’s get to the basic then.

As said before, the most common allergens are

  • Milk
  • Eggs
  • Soy
  • Fish
  • Shellfish
  • Wheat
  • Peanuts
  • Tree Nuts

In fact, those eight allergens make up for more than 90% of the food allergy reactions so it totally makes sense to start your elimination diet by cutting out these eight foods.

Most elimination diets also eliminate foods that are often associated with food intolerances such as

  • Gluten
  • Dairy
  • Sugar
  • Legumes
  • Caffeine
  • Alcohol
  • Citrus Fruits
  • Processed Foods
  • Hydrogenated Oils

It really is up to you whether you eliminate all of these foods, but keep in mind: Many people are gluten sensitive without knowing it. Eliminating gluten may help with leaky gut syndrome which can cause allergic reactions, autoimmune reactions and high levels of inflammation.

Due to pasteurization dairy products like milk, cheese or yoghurt may lack certain enzymes which can make them potential allergens.

Alcohol too can cause allergic reactions and may increase the growth of bad bacteria in the gut.

Products like soy are huge GMO crops. In general, you should avoid GMO if possible and for some elimination diets eating non-GMO is a key part.

Hydronic oils may cause chronic inflammation which may lead to other food intolerances.

Whatever it is you’re eliminating from your diet, always make sure to read food labels carefully. You want to avoid even the smallest trace of the things you cut out.

During your elimination diet, it is a good idea to create and maintain a food journal. Here you want to describe how you’re feeling and your symptoms like bloating, nausea, or diarrhea on a daily basis. Hopefully, after a while, you’ll start to report improvements.

When you start to reintroduce the foods again into your diet, documenting your symptoms is just as important. You can also start to compare symptoms after cutting them out and after reintroducing them. Be prepared for some stark differences between elimination phase and reintroduction phase. These indicate which food your body tolerates and which it doesn’t.

An elimination diet certainly requires discipline. But in the end, it is worth it. Many people don’t even realize they have an issue until they experience life without them. They think that their acne or headache is just part of who they are when in fact it is a certain food that they just don’t tolerate. Going through an elimination diet will help you find out.

Further Sources

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