How Are Allergies Connected to Your Cat’s Gut Health?

When your cat’s gut microbiome is out of balance, your cat can develop allergies. An allergy is an exaggerated immune response that causes uncomfortable symptoms like itchy skin, hives, sneezing, watery eyes, and recurring ear infections. Common allergy triggers include pollen, insect bites, and mold spores.

Health Tip


If you suspect your cat has food allergies or food sensitivities (intolerances), see this article and the Gut & Digestion page.

The gut microbiome is involved in allergies because 70%–80% of immune cells live in the gut. So if your cat suffers from allergy symptoms, rebalancing their gut microbiome can help. 

So what is the gut microbiome? It’s the community of bacteria, fungi, and other microbes that live in your cat’s digestive tract and are essential for good health.

How Does a Cat’s Gut Become Imbalanced?​

A gut microbiome is imbalanced when it’s missing good bacteria, has too many harmful bacteria, or doesn’t have enough diversity. When the gut is out of balance, immune functions stop working properly, making allergic reactions much more likely to occur. Factors like disease, age, diet, and medications—especially antibiotics—can cause this kind of imbalance in your cat’s gut. 

Missing Good Bacteria

Too Many Harmful Bacteria

Not Enough Diversity

How Can You Give Your Cat Relief Right Now?

For cats who suffer from irritated, itchy skin or other allergy symptoms that are chronic or severe, we recommend our KittyBiome™ Gut Restore Supplement.

The supplement introduces an entire community of beneficial cat-specific bacteria to add diversity and bring balance to the gut while relieving symptoms. Gut Restore is a fecal microbiota transplant (FMT) in an oral capsule. FMT has been shown to improve symptoms in cats with itchy skin and other allergic reactions. Replenishing any missing bacterial populations can often resolve symptoms quickly by restoring a healthy balance to your cat’s gut. If possible, we still recommend testing your cat’s gut microbiome with a Gut Health Test. 


For cats with occasional or mild allergy symptoms, we recommend our KittyBiome™ S. boulardii + FOS Powder, a probiotic plus prebiotic daily supplement.

With active ingredients Saccharomyces boulardii and Fructo-oligosaccharides (FOS), our  supplement designed for cats supports good digestion, strengthens the immune system, and promotes healthy skin. S. boulardii is a probiotic yeast with anti-inflammatory properties, and FOS is a prebiotic fiber that good bacteria like to eat. Studies in cats have shown that supplementation with FOS improves both gut health and immune functions.

How Can You Know What’s Going On in Your Cat’s Gut?

We recommend testing your cat’s gut microbiome with our at-home KittyBiome™ Gut Health Test.

Gut microbiome testing can give you a detailed understanding of what’s going on in your cat’s gut, revealing any imbalances that may be causing allergy symptoms. 

You send us a small poop sample from your cat, and we do the rest. Using DNA sequencing, our scientists analyze all the types of bacteria in your cat’s poop and compare them to our healthy cat reference set to determine if an imbalance is present. We then provide an interactive online report on your cat’s gut microbiome with personalized diet and supplement recommendations to help relieve symptoms and improve your cat’s gut and overall health. 

Health Tip


Feeding a healthy, balanced diet is the best way to manage your cat’s gut microbiome. If you’ve taken our Gut Health Test, follow the diet recommendations in your cat’s personalized report to support the growth of beneficial bacteria.

Since the microbiome is an ever-changing ecosystem that is impacted by multiple factors, including diet and medications, we suggest re-testing your cat’s gut health annually or anytime symptoms arise. A well-balanced gut microbiome will help your cat live a healthier, happier life.

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