The Importance of a Healthy Microbiome in Your Pet

If you have been a pet parent for years or even a few months, you have probably heard that gut health is essential to your pet’s overall health and wellbeing.  But what does gut health entail?  To understand how to maintain optimal gut health in your furry friend, an understanding of the gut microbiome and its function in the body is necessary. 

What is the gut microbiome?

The microbiome consists of microbes that are both helpful and potentially harmful. Most are symbiotic (where both the animal’s body and microbiota benefit) and some, in smaller numbers, are pathogenic (promoting disease). In a healthy body, pathogenic and symbiotic microbiota coexist without problems. These microbes are foundational to health in that they facilitate proper digestion, produce vitamins and other nutrients, protect the gut lining and support immune system function. The gut microbiome is considered the “second brain” of the body; a whopping 80% of the immune system is found in the microbiome.

All animals need a strong microbiome to get all the nutrients needed from the food they eat. The gut is the “conductor to the symphony” in an animal’s body - it tells all the organs what to do. 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. A dog or cat could be eating high quality, complete and balanced food and not get all the potential nutrition if the gut is imbalanced. 

What causes microbiome imbalance?

Diet plays an essential role. The food and treats you feed your pet can support a balanced gut, or contribute to its imbalance. Highly processed inferior food, especially heat processed kibble, will result in an inferior digestion process. Dogs and cats eating kibble are more prone to inflammation, resulting in metabolic consequences. Lack of diversity in the diet can also play a role in gut imbalance. Your dog or cat should receive most of his nutrients from a fresh, whole food meal plan that contains lots of dietary diversity. Different proteins and plant matter will carry different strains of good bacteria to feed the gut.

Cats, in particular, were not meant to eat anything dry. The cat species originated thousands of years ago in Egypt - a hot, dry climate. Ancient cats received their needed fluid (along with many nutrients) through the blood of their prey. The anatomy of a cat (short intestines) does not lend itself to digestion of dry food. Cats who eat kibble, even though they drink water, will suffer from gut and kidney disorders.

Medication – The most common veterinary-related cause of bacterial imbalances in pets is the use of drugs that disrupt the microbiome, including the continual use of anti-inflammatories (both steroidal and nonsteroidal), the routine application or ingestion of flea/tick pesticides, chemotherapy drugs, and of course, overuse of antibiotics. A recent “State of the Gut” survey shows that only 50% of pet parents were aware that antibiotics had an impact on gut health. The database in this study 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 sample, and that these animals were likely to have prior exposure to antibiotics and to experience chronic diarrhea.[1] Even occasional use of antibiotics can cause chronic microbiome imbalance and inflammation. When antibiotics are prescribed, they kill bad bacteria in the body, but they also kill many of the beneficial bacteria that live in the gut, on the skin, and in the respiratory tract.[2] Examples of infections that proliferate from antibiotic misuse include those of the skin, urinary tract, and respiratory system.[3]

Stress in both the pet and the pet parent plays a large role in gut health. Our pet’s emotions are very closely correlated to our own. Stress primarily affects the vagus nerve and sets off the “fight or flight” response in an animal. Energy needed for digestion is shifted to other systems to support a stressed animal. It is important for pet parents to take care of themselves before they take care of others.

What are symptoms of an imbalance in the gut?

The more common signs and symptoms include constipation, diarrhea, vomiting or regurgitation, increased and/or worse smelling flatulence, excessive drooling, reduced appetite, weight loss, blood, or mucus in the stools. Your dog or cat may be living with a gut imbalance and not show any outward signs and symptoms. Leaky gut, or dysbiosis, occurs when inflammation in the gut results in pathogens being released from the gut through the cells in the now permeable gut lining. The body will consider these pathogens foreign and try to attack them. Symptoms of leaky gut include itching and allergies, food intolerances, irritable bowel disease (IBD), and irritable bowel syndrome (IBS). Untreated dysbiosis can also result in yeast overgrowth, acid reflux, histamine intolerance, and mast cell tumors.

How can I restore gut microbiome balance in my dog or cat?

  • Feed a diverse, whole food, species-appropriate diet low in starchy foods. Rotating proteins and diets are the best defenses against malnutrition and dysbiosis. Every pet absorbs nutrients differently. Meat purchased in one area may have a different nutrition profile than meat purchased several hundred miles away. Take note of how your dog or cat responds to the seasons…from a Traditional Chinese Veterinary Medicine (TCVM) perspective, cooling foods such as duck, fish and rabbit can help with summer damp heat, while easy-to-digest, warming proteins such as chicken, lamb and venison can help to warm up the digestive system in the winter months.


  • Add prebiotics and probiotics to your pet’s feeding regimen and rotate them regularly. Prebiotics are a special type of fiber that feeds the good bacteria living in your gut. Examples of high-fiber whole food prebiotics include apple, banana, broccoli, and greens such as kale. If getting your dog to eat these foods is a challenge, use a well-researched, high-quality prebiotic that contains everything your dog needs.

Probiotics are live microorganisms that are intended to have health benefits when consumed. Probiotics should be given daily and rotated on a regular basis. Even when feeding a raw or gently cooked healthy organic diet, our pets are continually exposed to environmental toxins and the resulting stress will create a gut imbalance. The food we eat today is void of certain vitamins and minerals, and the nutrient profile will depend on the soil it was grown in. Different commercial probiotics will contain different strains of good bacteria. Probiotics that are compounded specifically for dogs and cats, as well as products containing wild strains of good bacteria are highly recommended. Product rotation will increase the diversity of good bacteria in the gut. Indoor cats especially need a probiotic for gut health. Cats in the wild get their good bacteria from natural sources by eating bugs and grass. Raw dairy products such as goat milk are an excellent source of probiotics, in that they contain beneficial bacteria passed from the animal.

  • Digestive Enzymes play a key role in breaking down the food your pet consumes. These proteins speed up chemical reactions that turn nutrients into substances that the digestive tract can absorb. The pancreas, gallbladder, and liver release enzymes; however, if the animal has a digestive disorder, the body will not make enough for nutrient absorption.  Adding digestive enzymes to your pet’s food can help make up for the deficit.


  • Herbs – In recent years, research studies have shown the value of medicinal plants. Pharmaceutical companies are aware of this research and are trying to get a share of the market, but largely, through creating and manufacturing synthetic versions of medicinal plant elements. Nature offers the entire plant, and there are many benefits that are not incorporated into conventional medicine because it is manufactured to target one plant element. The body responds to herbs by using all available elements of the plant to get rid of bad bacteria without the side effects of traditional medicine. Herbs for the gut have a systemic reach, assisting the gut as well as the liver. The specific herbs used to heal the gut will depend on the symptoms of the animal and the specific pathogens causing problems. Cooling herbs like aloe (powder), slippery elm, and marshmallow root are best for animals with a warm or hot constitution. Yarrow is good for food sensitivities, prevents stagnation in the gut and can be given to animals with both a warm/hot and cool/cold constitution. Plantain helps good bacteria adhere to the gut wall and reduces inflammation. Warming herbs like St. John’s Wort calms reactivity and food sensitivities in the gut. Olive leaf extract is an antifungal and anti-viral microbiome balancer and can be used in the treatment of Ehrlichiosis. Turmeric is a great herb for yeast and leaky gut and helps detoxification. Ginger helps with all common gut issues, reduces nausea, and calms inflammation. Milk thistle is good for liver detoxification and anal gland problems. Nettles are good for kidney, gut and liver health and add needed minerals. Licorice root is neutral, good for all gut problems, and works with other herbs to increase their efficacy. 


  • Fecal Microbiota Transplantation (FMT) is a procedure in which the fecal matter from a healthy donor is transplanted into an animal affected by gastrointestinal disease. Research studies about FMT application in veterinary medicine are few, but veterinarians that perform the procedure report substantial improvement in gastrointestinal diseases such as IBD.


  • Testing - Nutrient testing is a valuable tool. For example, animals with chronic GI disease are often depleted in vitamin B. Supplementation can help eliminate vitamin deficiency.  Advanced home test kits can identify gut inflammation, leaky gut and other factors that contribute to gut dysbiosis. Fecal samples are sent to a lab for testing and evaluation. Some labs will go a step further and recommend steps to correct the microbiome imbalance. These tests can be used for animals with chronic issues to pinpoint the source of the problem in the digestive system. They can also be used in healthy dogs so that parents can be proactive in treating problems before they become advanced.

Cat and dog owners, while interested in the gut health of their pets, often find it challenging to navigate the wealth of information that is available. Maintaining gut health in your pet is as simple as feeding them a species-appropriate whole food diet (including treats), limiting the use of medications including antibiotics and flea & tick products, reducing stress, and minimizing exposure to toxic chemicals. These actions form the foundation of a proactive plan to keep our pets thriving with a balanced and healthy gut microbiome. 





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