menu iconknow your dna logosearch icon
Gut Health and Allergies
Updated on October 31, 2023
Back to top
back to top icon
Gut Health and Allergies

Gut health is one of the most important yet overlooked aspects of feeling your best. Your gut affects all aspects of your health and well-being.

Many things affect your gut’s health, too. One of the most prominent links is between your gut health and allergies.

Studies show that people who have less diverse gut bacteria and poor gut health tend to be more prone to developing allergies.1 

This, of course, depends on a series of factors. Some people may need antibiotics more than other people, which can kill off even beneficial bacteria in the gut, among other reasons.

Still, diverse gut bacteria can keep food allergies (or even inhaled allergens, like pollen) at bay or even help dampen their effects. Your gut microbiota requires a variety of bacteria to help you feel your best. For the most part, a good variety in your gut microbiome means less severe or even fewer allergies altogether.

Gut microbes may be essential to understanding why you develop allergies and how to overcome them.2

This is why taking good care of your gut health and diversifying the gut bacteria in your gastrointestinal tract will be beneficial.

Gut Health and Allergies 4

What Causes Food Allergies and Intolerance?

Allergies and intolerances are caused by hypersensitivity to certain foods or substances.

You are not born with allergies or intolerances. Rather, you develop them as you grow older. When your body recognizes something as a threat (even if it isn’t or wasn’t previously), it triggers an inflammatory response.

Problems with a leaky gut often lead to food intolerances or allergies. These allergies develop when acid, bacteria, and food molecules leak into your bloodstream and wreak havoc.

Researchers believe that chronic inflammation plays a role in gut health.3 The more inflammation there is in your body, the more toxins seep into your bloodstream. This further exacerbates inflammation and becomes a vicious cycle.

What’s worse is that most modern diets lack proper nutrients, and lifestyles are filled with stress. Poor diet and stress negatively interfere with healthy gut bacteria. It makes it difficult for the body to digest food properly.

The bottom line? Allergies, both to certain foods and seasonal allergies, and gut health are connected. Food intolerance and gut health are also connected.

Know Your DNA Reviews

Best Gut Health Test

Our review of the best at-home Microbiome Tests.

What are Food Allergies?

Food allergies occur when someone eats something and experiences an adverse physical reaction.

This is due to antibodies recognizing a food or substance as a threat, and your immune system reacts in severe ways.

Food allergies (and even inhaled allergies) can cause severe damage to your body and can even lead to death without proper medical supervision and intervention.

The most common food allergies are:

  • Fish and shellfish
  • Peanuts
  • Nuts
  • Eggs
  • Milk
  • Wheat
  • Soy
Gut Health and Allergies 5

Some non-food or seasonal allergies are:

  • Dust/dust mites
  • Grasses, weeds, and other plants
  • Pets and dander
  • Certain medications
  • Insect stings
  • Pollen
  • Mold
  • Latex

This isn’t a comprehensive list. There are cases of uncommon allergies, such as red meat. The best way to determine them is to undergo allergy testing. 

Any food or external substance can trigger an adverse physical reaction, but that doesn’t mean they’re automatically a food allergy. Food allergies are often more severe and life-threatening compared to intolerances or sensitivities. 

Signs and symptoms of a mild allergic reaction include: 

  • Stuffy nose - When you suffer from allergies, you will often trigger a release of chemicals in the mucous layer of your nose. The layer becomes inflamed and often overproduces mucus.
  • Sneezing - Because your body recognizes the allergen as a foreign substance, your nose is alerted to sneeze in order to eject any foreign contaminants.
  • Watery eyes - Some allergens cause blood vessels in the eyes to swell, making your eyes water and itch.
  • Stomach pain - When your body releases histamine as a result of an allergic reaction, it can cause abdominal pain. Histamine build-up can cause painful contractions.
  • Nausea - Histamine often lands on the brainstem where receptors connected to your vomit response are triggered.
  • Diarrhea - Painful contractions that occur in your body because of histamine release can cause diarrhea. 
  • Hives - Histamine release as an allergic reaction can cause capillaries to swell, causing welts filled with fluid on the skin.
  • Itchiness/rash - Similar to hives, histamine release can cause itchiness and wheals to rise on the skin.

More severe allergic reactions include anaphylactic shock, which is cause for emergency. During anaphylaxis, the airways are constricted and can cause you to suffocate or suffer heart damage. Anaphylaxis can cause death.

What’s the Difference Between a Food Allergy and an Intolerance?

Food allergies happen when the immune system responds to a food it thinks is a foreign substance. Intolerances do not involve the immune system whatsoever, and occur when the body has a difficult time digesting certain food.4

Intolerances do not show up in allergy tests. They are also not life-threatening, unlike allergies.

People also assume allergies are worse than intolerances. This is sometimes the case, but not always. It depends on how long it takes for the adverse reaction to develop that determines if an issue is an intolerance or allergy.

A food allergy triggers an immediate response. It involves a systemic immune reaction because the body sees the substance as a dangerous foreign invader. The immune system kicks into overdrive and responds immediately or within a few minutes.

An intolerance, on the other hand, takes hours to manifest. As the offending food moves through the digestive system, symptoms arise. Intolerances are not immune system reactions, they are digestive.

What Causes Food Intolerance?

Intolerance is caused by the body’s inability to digest certain foods. Food intolerance means the body isn’t able to digest the food properly.

It triggers unpleasant digestive symptoms. There is no risk of anaphylactic shock. However, there are instances in which food intolerances still cause secondary medical emergencies.

Some symptoms of food intolerances overlap with some allergy symptoms, which is why people sometimes mix up the two. Some symptoms are:

  • Abdominal pain
  • Gas and bloating
  • Diarrhea
  • Nausea
  • Fatigue
  • Heartburn

Remember that intolerances are not immediate and often manifest hours after ingesting food.

Gluten Intolerance

Gluten sensitivity or intolerance is an issue that has gotten a great deal of attention in recent years. 

Gluten intolerance is when your body reacts negatively to food with gluten in it.

It’s often linked to celiac disease, which is a severe form of intolerance. Someone with celiac disease must eliminate all forms of gluten-containing foods from their diets.5 While they’re closely linked, they are not the same. 

Being gluten intolerant doesn’t always mean you have celiac disease. Celiac disease is an autoimmune disorder. Intolerances are not disorders.


There is also a genetic component to food intolerances and food allergies. 

For example, lactose intolerance occurs at much higher rates in the East Asian community. There is also evidence of higher rates of alcohol intolerance within this same community. 

Food allergies and intolerances themselves can be passed down. It’s also possible that certain groups tend to favor certain foods in their diet, causing similar patterns in terms of gut microbiota. With similar gut microbiota, similar food allergies and intolerances can be developed.

A variety of unpleasant symptoms occur when a person’s system cannot properly break down a substance. These include an upset stomach, stuffy nose, and a red flush. These substances irritate the gastrointestinal tract and affect the entire body negatively. 

Problems in the Gut Microbiome

Most of the time, food intolerance is caused by an imbalance in the gut microbial environment. The human gut microbiome is home to trillions of bacteria. To ensure the gut’s optimal health, a balance must exist in the gut flora. Harmful bacteria should never outnumber beneficial bacteria.

To learn more about your gut health, there are human gut microbiome tests that you can take at home.

The Everlywell Food Sensitivity Test kit tests your body’s immune response to 94 different types of food. Their Food Sensitivity Comprehensive Test Kit tests measures your immune cells’ response to 204 food types.

If your gut bacteria are imbalanced or have little diversity, you may have a tendency to develop more food allergies, intolerances, or sensitivities.

Treating Allergies

If you suspect you have a food allergy, your doctor will conduct a test to identify the allergy.

There are medications available to manage the symptoms of the allergy. However, in many cases with food, it’s best just to avoid the food.

Should you accidentally come into contact with the food you are severely allergic to, carrying an Epipen (an epinephrine autoinjector) is the best way to manage potentially deadly symptoms. Epipens relax the muscles so your airway doesn’t constrict too tightly to the point of potentially suffocating you. 

Gut Health and Allergies 6

It’s easiest to just eliminate the food allergies from your diet to save your immune system the trouble.

Treating Intolerances

Managing intolerances often comes with avoiding the food you are sensitive to altogether, like you would with a food allergy.

Eliminating foods you are intolerant of from your diet is the safest and easiest course of action.

Otherwise, if you unknowingly ingest food you’re intolerant of, you can take some over-the-counter medication like antacids to minimize the digestive symptoms. People with lactose intolerance can also take lactase enzymes before consuming dairy.

How Gut Microbiota Composition Can Influence Food Allergies

Your gastrointestinal tract is home to a host of different gut microbes. This is called the gut microbiome or the gut microbiota. 

Studies have shown that many who have very little gut bacteria diversity have a higher tendency to develop food allergies. So your gut microbiota and gut bacteria composition are huge factors of whether or not you’ll react to certain foods.

Diverse and balanced gut bacteria help with immune protection.6

Imbalance in your gut bacteria (gut dysbiosis) can often lead to increased inflammation (like inflammatory bowel disease) and allergic responses. This is because imbalances in the gut may throw off the immune system and cause it to respond less potently when faced with threats.

So when a food allergy triggers the immune system to respond and the gut is already out of sorts, it can exacerbate the reaction.

If your immune system isn’t in optimal condition due to gut dysbiosis, you may feel even more severe symptoms of food allergies, such as:

  • Tightening of airways
  • Anaphylaxis
  • Heartburn or chest pain
  • Abdominal pain

This is why diversifying your gut bacteria and keeping it balanced is integral. It’s connected to your immune system and will play its part in protecting you when a foreign substance or food allergy enters your body.

With strong, healthy, and diverse gut bacteria, you can dampen allergic reactions and strengthen your immune system.

Factors That Affect Gut Microbiota Composition

The following can also shape your gut bacteria:6

  • Genetics – Family members are more likely to have similar gut microbiota composition
  • Birth delivery – The gut bacteria you will grow may be influenced by how you are delivered—if delivered vaginally, you may acquire bacteria that live in the vaginal area
  • Breast milk – Breast milk contains natural prebiotics that will promote good bacteria growth

How Does Gut Health Affect the Immune System?

The gut microbiome has been linked to almost all the organ systems in the body. It affects mental health, appetite, and even the immune system.

The immune system is what we rely on to fight bodily invaders and repair any damage they may cause.

When you ingest food, you are introducing elements to your body. Ingesting something is one of the easiest ways for a foreign contaminant to enter your body, and so the immune system is attuned to the gut for this reason.

Most of your body’s immune cells live in the gut. With an unhealthy, imbalanced gut, you are compromising your immune cells and their ability to fight off threats. This may cause the immune system to overreact or underreact, causing inflammation or even more severe allergic reactions.

Your gut microbes must be diverse and balanced to keep your immune cells healthy as well.

Gut Microbiota Analysis

You can analyze your gut microbes through these methods:

  • Feces samples
  • Throat samples
  • Stomach samples
  • Endoscopy samples
  • Biopsies

These samples will provide a snapshot of your gut microbiome. The bacteria in your gut will live on in these samples and show you what it may look like inside your body. Not all bacteria may show up, however, so remember that these analyses may not be completely accurate.

This partial picture will at least give you a glimpse into your overall gut health and what you may want to do to diversify your bacteria.

What Can You Do If You Have Food Intolerances and Allergies?

Being intolerant or allergic to some types of food is not a death sentence.

It should not get in the way of you enjoying life. When it comes to diet and lifestyle, there are some things that you can do to manage these conditions. Here are some of them:

Dietary changes 

This is the best option available for dealing with food intolerances and allergies. Avoid eating foods that you know will trigger symptoms in you.

Having a healthy gut is your strongest defense against trigger problems with foods.

There is evidence that people with a healthy gut microbiome have a much lower risk of experiencing food allergies. There is also evidence that the increase in food allergies is linked to the modern diet damaging gut health. 

As our guts get less healthy, instances of food allergies rise.

Lifestyle Changes

The evolution of our lifestyle has led to an increase in allergies.

For example, people who eat a smaller variety of foods tend to be prone to an allergic response. Lack of exercise and time outside also affects gut health.

It increases the risk of developing problems with food. There’s even evidence that breastfed children have a diminished risk of allergies because breast milk contains so many healthy microbes for the gut.

Do Probiotics Help with Allergies?

Probiotics contribute colonies of good bacteria to your gut that can help diversify your microbiome. With a higher diversity of microbes, you can strengthen your immune response.

What is the best probiotic for allergies?

If you have allergies, here are some of the best probiotic strains you can introduce to your gut to dampen your immune response:

  • Lactobacillus rhamnosus
  • Bifidobacterium infantis
  • Bifidobacterium longum

These probiotics don’t just contribute to the colony-forming process in your gut, they also inhibit histamine release, which is what causes a lot of the more severe and uncomfortable allergic reactions.

What’s the Best Way to Reduce Your Risk of Allergies?

There are a few things you can do to reduce the risk your body will react poorly to certain foods.

Know your risk

Understanding your genetic risks of developing food allergies and intolerances gives you a starting point for better managing your diet

You can watch for symptoms and make adjustments based on your specific circumstances.

Improve your gut health

The best way to do this is to cut out processed foods and replace them with gut-healthy whole foods. Gradually increasing your intake of foods high in healthy bacteria strengthens your gut health. 

Making healthy choices regarding your diet and lifestyle choices helps you restore gut health and reduce the risk of an adverse reaction to foods. Avoiding antibiotics or only using them when absolutely necessary is also important. 

Although you want to start eliminating foods from your diet that could be problematic, eventually, you’ll want to include a lot of diversity.

Eat a wide range of gut-healthy food

Do what you can to improve the good bacteria and probiotics in your diet. 

If you want to reduce your child’s risk of developing a gut health problem, exposure to various foods during childhood is important.

Invest time in understanding your body

Your body is unique, and there might be foods that don’t agree with you. Accept that what works for other people might not be suitable for you. 

Furthermore, your body changes as you age. A food that you were once able to eat might be intolerable as you grow older. Be willing to adjust. 

The better you learn to feed your body, the better you’ll feel. This lessens your risk of having long-term health complications linked to your diet.

Some Common Questions About Gut Health and Allergies

Are allergies related to leaky gut?

Some of them are related, but not all of them. Leaky gut deals with leaks into the bloodstream that can cause allergies.

Allergies are immune responses to foreign contaminants.

Can Inflammatory Bowel Disease Make Allergies Worse?

Inflammation can make allergic reactions more severe, as the immune system is not in optimal condition.

Know Your DNA Reviews

Best Microbiome Test

Looking for the best microbiome kit on the market? Look no further! Our review round-up page has all the information you need to make an informed decision.

Updated on October 31, 2023
Kelly Jamrozy
Kelly Jamrozy
Content Contributor
Kelly has experience working with clients in a variety of industries, including legal, medical, marketing, and travel. Her goal is to share important information that people can use to make decisions about their health and the health of their loved ones. From choosing the best treatment programs to improving dental and vision health to finding the best method for helping anyone who is struggling with health issues, she hopes to share what she learns through informative content.
Back to top icon