Most people don’t realize their gut plays a major role in managing allergies. 

Trillions of bacteria in your gut microbiome influence immune responses, potentially making allergies worse—or better. Research is now showing how the balance of these bacteria impacts inflammation and allergic reactions. 

Understanding this connection is the first step toward taking control of your allergies.

The Gut Microbiome: Your Body’s Immune Control Center

The current research suggests that your microbiome can make food allergies better or worse, depending upon the actual bacteria that are identified.

Some research shows that strains of bacteria like Clostridium help you to improve your food allergies or make you less susceptible to them. Emerging evidence also shows that changes in the quantity or diversity of gut microbes play a key role in immune regulation and can either enhance oral tolerance or increase susceptibility to food allergies. For example, overgrowths of harmful bacteria can lead to increased permeability of the gut lining, often referred to as “leaky gut,” allowing allergens to interact with your immune system in ways they shouldn’t.

Here’s what you can do to improve your gut microbiome: Prioritize diversity in your diet and probiotics.

With the current research, we just don’t know if there’s a single bacteria to concentrate on to eliminate allergies or allergy-like symptoms. This is why we use this shotgun approach to probiotics—introducing multiple strains—and it is currently one of the most effective ways to improve gut health. Additionally, probiotics, especially strains like Clostridia, have shown promise in preventing or resolving allergic symptoms in both animal models and clinical trials.

By adding diversity, you’re essentially giving your gut a toolkit to fight off allergens and other atopic diseases like asthma and allergic rhinitis.

Eosinophilic Esophagitis (EOE): The Allergy-Gut Connection

EOE is a lesser-known condition that blurs the lines between gut health and food allergies. 

It involves an overproduction of eosinophils—a type of white blood cell—in the esophagus, leading to inflammation in the gut. The two most common causes of having food-induced EOE are milk and wheat, even when traditional allergy tests don’t show a reaction. So when your EOE gets out of balance, you can start exhibiting food allergies or symptoms that are like a food allergy.

New cases for EOE range from 5 to 10 cases per 100,000 people. When you figure out people that have already been diagnosed, then it comes down to 1 in 1,000, which is fairly significant.

To solve this condition, elimination diets are key.

Start by cutting out milk and wheat for 6 to 8 weeks and monitor for improvement. For severe cases, medications like Dupixent or budesonide slurries may be necessary to manage inflammation.

Enzyme Deficiencies and Misdiagnosed Allergies

Sometimes, what appears to be a food allergy is an enzyme deficiency. 

The gut relies on enzymes, like disaccharidases, to break down food. If your body lacks these enzymes in the gut wall, then bacteria will break down the disaccharidases you eat, causing you to have bloating and gas that mimic food allergy symptoms. 

The solution? Testing. 

A biopsy of the gut lining, conducted by a gastroenterologist, can confirm whether you’re dealing with an enzyme deficiency. If diagnosed, adjusting your diet and enzyme supplementation can dramatically reduce symptoms.

Ensuring a healthy gut sets the stage for improved digestion and a stronger defense against allergy-like symptoms, paving the way for a comprehensive approach to gut-related health issues.

Four Actionable Steps to Improve Gut Health and Allergies

As an Allergist with 30 years of experience, here are four simple steps I recommend to take control of your gut health and reduce allergy symptoms:

1. Change Your Probiotics Monthly – Switching probiotic strains ensures your gut gets a wide variety of beneficial bacteria.
2. Change Your Diet Every Three Months – You can adopt a Low FODMAP Diet to start, which limits fermentable carbohydrates that can worsen conditions like SIBO and EOE.
3. Increase Fiber Gradually – Start with plant-based fibers like flaxseeds or try a supplement like Metamucil to feed beneficial gut bacteria while promoting regularity and reducing bloating.
4. Exercise Regularly – Physical activity has been shown to positively impact gut microbiome diversity, enhancing immune function.

While there’s no one-size-fits-all cure for allergies related to gut health, and there is more research needed to understand the full relationship between gut health and allergies, taking a proactive approach can make a difference. 

By focusing on bacterial diversity, addressing underlying conditions like SIBO or EOE, and making strategic dietary changes, you can reduce symptoms and improve your overall well-being. Start small. Change your probiotics, tweak your diet, and consult with an expert allergist like myself or a gastroenterologist. 

The path to better gut health and fewer allergies begins with informed action—and it’s worth every step.

(p.s., if you have questions about food allergies or need expert care, reach out to me here)