Your Dog and Cat’s Gut Health Microbiome – Why It’s So Important

You’re probably aware that gut health is key to your dog or cat’s overall well-being, but may need some guidance on understanding their microbiome and how to support it.

How much do you know about your dog or cat’s gut health? A recent survey of cat and dog parents uncovered a disconnect between an awareness that gut health is important for the health of our animals, and an understanding of how to support and maintain it. Most animal parents know that gut health is essential for overall health, but don’t know about the microbiome and its role in establishing and maintaining gut health.


The gut microbiome is a community of bacteria, fungi, and other microbes that live in your dog or cat’s digestive tract. These microbes are foundational to health; among other things, they contribute to proper digestion, produce vitamins and serotonin, protect the gut lining, and support immune system function.

When this community is disrupted, a number of symptoms can emerge. A gut microbiome becomes imbalanced when it is missing beneficial bacteria, has too many harmful bacteria, or does not have enough diversity in the types of bacteria. Itchy skin, vomiting, diarrhea, constipation, and bad breath can all indicate an imbalance in your animal’s gut microbiome. When your dog or cat’s microbiome is out of balance, some of the gut’s important functions don’t work as well.


Factors like disease, age, diet, and medications can cause long-term disruption of the gut microbiome, and may be contributing to the digestive and skin conditions affecting over 60 million cats and dogs in the US. Fortunately, a number of approaches can be taken to monitor, restore, and support gut health, such as gut microbiome testing, providing a healthy diet, and using supplements when possible to reduce the use of medications.


In an effort to promote awareness of the significance of gut health, we conducted a survey of 2,000 cat parents and 2,000 dog parents. They were asked what they think about gut health in general, how it might affect their animals’ wellness, and what they can do to support and improve gut health. We also compiled seven years of information from our microbiome database, revealing trends in the bacterial makeup of the microbiome of cats and dogs. We presented the findings in The State of the Gut Report1 (available as a free download). Most people are aware that gut health matters for their animals’ overall well-being, but aren’t sure what they can do to better support gut health.


Feeding your dog or cat a healthful diet helps prevent common illnesses; supports and boosts the immune system; and positively influences the composition and function of bacteria living in his gut microbiome. However, many people are unaware of the connection between diet and gut health. In our survey, we found that nearly one in three animal parents did not know that diet plays an essential role in gut health. Even fewer realized that treats, which may seem insignificant compared to the daily diet, can also affect the structure and function of the gut microbiome. An appropriately balanced diet is an important way to maintain the gut microbiome by supporting beneficial bacteria and discouraging harmful bacteria from populating the gut.


While antibiotic treatments are sometimes necessary, antibiotic use has been shown to cause detrimental — and sometimes long term — changes to the gut microbiome. Many antibiotics reduce both beneficial and harmful gut bacteria, and this can allow opportunistic pathogens like E. coli to flourish, promoting inflammation and causing clinical signs. Nevertheless, only 50% of surveyed animal parents were aware that antibiotics had an impact on gut health.


We also asked people to report any exposure to risk factors that could have negatively impacted their animals’ microbiome over a 12-month period. Not surprisingly, exposure to antibiotics was one of the two top risk factors reported for both dog and cat parents. A change in diet was another top risk factor associated with gut imbalance.

There are many different kinds of microbes in a dog or cat’s gut microbiome, and each requires certain nutrients to survive. Some specialize in digesting complex carbohydrates, others digest proteins, and some thrive on sugar. As a result, the macro-nutrients (carbohydrates, fats, proteins, and fibers) in the food an animal eats influence which bacteria thrive in their gut.

When a diet has an overabundance of one macronutrient versus another, it can shift the natural balance of the gut bacteria, leading to an imbalance or dysbiosis. For example, bacteria in the Prevotella genus play fundamental roles in the breakdown of carbohydrates in food. However, if an animal’s diet is too high in carbs, and has insufficient protein, Prevotella can overwhelm the gut microbiome.

As another example, elevated levels of protein in a diet that lacks sufficient fiber can cause bacteria in the Fusobacterium genus to overgrow. In both situations, elevated levels of these beneficial groups of bacteria can lead to GI distress.

By looking at data gathered from our microbiome database (composed of over 60,000 samples), we found that one in three dogs and one in seven cats — both symptomatic and asymptomatic — had unhealthy levels of E. coli in their fecal microbiome samples, and that these animals were likely to have prior exposure to antibiotics and to experience chronic diarrhea.2


Our State of the Gut survey revealed that people truly care about the gut health of their dogs and cats, but many find it challenging to navigate the world of diets, nutrition, medications, and supplements. We recommend finding a veterinarian who uses gut microbiome testing and makes recommendations you can follow to support your own animal’s gut health and, in turn, their overall health.

1 State of the Gut. 2022.

2 Jessica K. Jarett, Dawn D. Kingsbury, Carlton X. Osborne, Alex L. Martin, Jonathan A. Eisen, and Holly H. Ganz. 2020. Defining Healthy: The Utility of Building a Companion Animal.


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