Is Your Gut Microbiome Affecting Your Allergies?

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Last updated: April 15, 2026

Are your allergies worse than ever, no matter what you do? Are you avoiding triggers, taking medication, and following your doctor’s orders, and yet you are still struggling with symptoms? While many factors contribute to allergies, one area that is often overlooked is your gut microbiome.

 

 

Your gut microbiome influences:

 

 

  • Inflammation levels 

 

  • Nutrient absorption 

 

  • Hormone balance 

 

But how does the gut connect to allergies? Let’s break it down.

 

What is the Gut Microbiome?

 

Your gut microbiome is a microscopic world within the world of your body. It is a collection of trillions of microorganisms (bacteria, fungi, etc.) that live in your digestive system, specifically in your intestines. These microbes help digest food, aid in producing some vitamins, and, most importantly, regulate your immune system. Your gut is your largest immune system organ, containing up to 80% of your body’s immune cells (Cleveland Clinic, 2023). Every person’s gut is unique to them. Babies receive their first gut microbes during vaginal delivery or breastfeeding. Later, your diet and environment introduce microbes. Some exposures can be harmful and deplete your gut microbiota.

 

How a balanced microbiome supports immune health:

 

  • Good bacteria help to develop regulatory T-cells, which prevent excessive immune reaction 

 

  • The microbiome produces short-chain fatty acids that reduce inflammation and support immune tolerance 

 

What is the Problem with an Imbalanced Microbiome?

 

A disrupted gut microbiome (dysbiosis) can lead to an overactive immune system, increasing allergy risk. What can cause this imbalance? If you’re like most people, you have probably encountered at least a few of these microbiome disruptors. 

 

  • Frequent antibiotic use 

 

  • A diet low in fiber and high in processed foods 

 

  • Chronic stress 

 

  • A lack of fermented foods in your diet 

 

  • Insufficient exposure to beneficial microbes (e.g. from outdoor environments or pets)

 

Each of these factors can reduce microbial diversity, weakening immune tolerance and making you more prone to allergic reactions. 

 

How the Gut Microbiome Affects Allergies

 

  • Dysbiosis increases inflammation. An imbalanced gut microbiome triggers low-grade inflammation, making the immune system hypersensitive to allergens like pollen, pet dander, or certain foods. 

 

  • A weakened gut barrier allows allergens to pass into the bloodstream. This can lead to a heightened immune response and increased allergic symptoms.

 

  • Low microbial diversity is linked to asthma, eczema, and food allergies. Studies have shown that food allergies have been increasing at an alarming rate of 6.5% (5% of adults and 8% of children). Of these food allergies, 90% are caused by the big 8 (cow milk, eggs, fish, shellfish, tree nuts, peanuts, wheat, and soybeans) and the microbiota has been shown to play a part in the development of food allergies (Suther et al., 2020). 

 

  • Gut bacteria influence histamine levels. Some microbes break down histamine (which triggers allergy symptoms), while others produce more histamine. An imbalance can worsen allergic reactions.

 

 

How to Support a Healthy Microbiome

 

 

Now that you understand how the gut microbiome affects allergies, what can you do about it? Here are some ways to support gut health and potentially reduce allergic reactions: 

 

  • Eat more fiber. Prebiotic-rich foods (bananas, garlic, oats, asparagus) feed beneficial gut bacteria. 

 

  • Incorporate fermented foods such as yogurt, Keifer, kimchi, sauerkraut, and pickles to introduce probiotic foods that enhance microbiome diversity. 

 

  • Avoid excessive antibiotics (when possible). While antibiotics are life-saving, overuse can disrupt gut bacteria. 

 

  • Reduce processed foods and added sugars. A high-sugar, low-fiber diet promotes inflammation and weakens gut health.

 

 

  • Consider probiotics. 

 

Taking care of your gut microbiome could be a missing piece in managing your allergies. What small change can you make today to support your gut health?

 

 

 

References 

Cleveland Clinic. (2023, August 18). What Is Your Gut Microbiome? Cleveland Clinic. 

Suther, C., Moore, M. D., Beigelman, A., & Zhou, Y. (2020). The Gut Microbiome and the Big Eight. Nutrients, 12(12). 

Tomkovich, S., & Jobin, C. (2015). Microbiota and host immune responses: a love-hate relationship. Immunology, 147(1), 1–10. 

‌Zubeldia-Varela, E., Barker-Tejeda, T., Obeso, D., Villaseñor, A., Barber, D., & Pérez-Gordo, M. (2022). Microbiome and Allergy: New Insights and Perspectives. Journal of Investigational Allergology and Clinical Immunology, 32(5), 327–344. 



Written By: AZ Dietitians
Published: April 28, 2025

Last updated: April 15, 2026

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