Learning About Restoring Your Pet's Microbiome

Restore Your Dog’s Microbiome.

How to Restore and Improve Your Pet’s Gut Health?

If your pet suffers from digestive or skin problems, the search for a solution can be frustrating. You’ve probably researched online, switched foods, tried prescription medications, and bought various supplements. But while many pets’ symptoms do improve in response to dietary changes or medication, other pets may experience only minor improvement (at best). Or their symptoms may go away but return after only a few weeks or months.

A key factor that may affect how your pet responds to treatment is the status of their gut microbiome — the community of microorganisms living inside the gastrointestinal (GI) tract, including bacteria, fungi, viruses, and protozoa (protists).

There is substantial scientific evidence that many health conditions — including inflammatory bowel disease (IBD), “leaky gut” syndrome, chronic diarrhea, allergies, atopic dermatitis, ulcerative colitis, and antibiotic-resistant Clostridium and Clostridioides infections (including C. diff infections) — have an element in common: an imbalanced gut microbiome.

What Is a Gut Microbiome Imbalance?

Research suggests that a diverse, well-balanced gut microbiome supports overall health and longevity by making your dog and cat more resilient to disease, environmental factors, parasites, and other potential threats to their wellness.

But many factors — including diet, pathogens, and medications (like antibiotics and steroids) — can disrupt your dog’s & cat's gut microbiome, leading to worrisome symptoms like diarrhea, constipation, bloating, weight loss, obesity, or itchy skin.

In many cases, pets with digestive problems, skin issues, or other symptoms are missing certain gut bacteria they need for healthy digestive and immune functions. Sometimes these beneficial bacteria are missing because they didn’t get passed along in their mother’s milk. Other times, “good bacteria” go missing because they are killed by antibiotic use or crowded out by the overgrowth of a pathogen (“bad bacteria”).

When all the beneficial gut bacteria your dog and cat needs aren’t present in the right numbers, the microbiome is out of balance. As a result, some of the gut’s important functions may stop working, leading to a variety of uncomfortable symptoms. Luckily, even in cases of serious imbalance, it is usually possible to restore the microbiome to a healthier state.

What Can You Do to Restore Your Pet’s Gut Health?

If your dog and cat suffers from the effects of a gut microbiome imbalance, restoring their gut health might require (a) adding beneficial bacterial groups that are missing, (b) removing harmful groups, and/or (c) rebalancing the existing bacterial populations to achieve healthier proportions.

There are many ways to restore diversity, strength, and balance to your pet’s gut microbiome. Some of the main approaches involve diet, prebiotics, and fecal microbiota transplantation (FMT).

This chart explains common microbiome conditions, potential causes, and ways to shift the microbiome:

Your Pet’s Diet Impacts Their Gut Health

Diet is the primary way to manage your pet’s gut microbiome. Good nutrition is one of the cornerstones of overall health and can help prevent common illnesses, boost the immune system, and positively influence the gut microbiome. There are thousands of different kinds of gut bacteria in your pet’s microbiome, and each kind requires certain nutrients to survive. Therefore, the food your cat and dog eats will influence which groups of bacteria thrive in the gut. Simple changes to your cat’s & dog's diet might be enough to restore balance.

Here are some things to consider when thinking about your pet’s diet:

  • Feed Enough Protein

Cats are obligate carnivores (meaning they have to eat meat to survive). For dogs, despite their long association with humans, dogs are still more carnivore than true omnivore, so both species, they need a diet that’s high in protein and low in carbohydrates. Adding more protein to your dog’s & cat's diet also supports the growth of the important Fusobacteria group, which do best in a high-protein environment.

If you’re feeding a diet that is nutritionally well balanced and yet your dog and cat still has digestive or skin health issues, it is possible that a food sensitivity (an intolerance or an allergy) is to blame. Food intolerances are quite common and can often be resolved by changing your dog’s cat's food. It is important to talk to your veterinarian before changing your pet’s diet, as some diets have been linked with certain health issues and to transition to new foods very gradually.

  • Avoid Diets That Are High in Carbohydrates 

Many kibble diets are too high in carbohydrates, so they don’t promote the growth of all beneficial bacteria. In a study where dogs were fed a high-protein, low-carbohydrate dog food, the microbiomes of overweight dogs shifted significantly, with important bacterial groups achieving the balanced numbers seen in dogs of a healthy weight. High-carbohydrate diets can also promote chronic inflammation, which may lead to additional health issues throughout the body.

The food you choose for your pet should contain at least 35% protein for dogs and 40% protein for cats on a “dry matter” basis. Also, be aware that diets labeled “grain free” or “gluten free” can still contain high levels of carbohydrates. Use this calculator to find the hidden amount of carbohydrates in your pet’s food.

  • Add Fermented Foods

Fermented foods — like yogurt, kimchi, kombucha, and sauerkraut — are probiotic foods, meaning that they are rich in live microorganisms (“good bacteria”) that are known to benefit human health. In small quantities, fermented goat milk is one probiotic food that also offers health benefits for pets. The kinds of bacteria found in goat milk and other fermented foods can help maintain a healthy pet’s gut flora, but they can’t provide the microbial diversity needed to correct an imbalance (dysbiosis).

  • Feed a Variety of Whole Foods Rich in Antioxidants

Antioxidants are compounds that support the immune system and prevent disease by getting rid of free radicals (reactive molecules that can damage the body’s cell membranes and even its DNA). The antioxidants found in food are typically polyphenols, which are produced by plants. These compounds feed beneficial gut microbes, increasing their numbers and also causing them to produce new substances (postbiotics) that promote the health of the whole body.

In people, higher intake of antioxidant-rich foods, such as fruits and vegetables, is associated with a lower risk of diseases related to chronic oxidative stress (such as glaucoma, cancer, Parkinson’s, and Alzheimer’s). Consider the ingredients included in your pet’s food and then talk with your veterinarian about how to add more antioxidant-rich foods to their diet.

  • Provide Adequate Fiber

Fiber also comes from plants (such as whole grains, vegetables, and fruits) and is another important element of your pet’s diet. Many soluble fibers are fermentable, which means the bacteria in the gut can consume them as a source of energy. Soluble fiber also helps keep your pet’s blood glucose at a healthy level. Insoluble fiber holds on to moisture and helps your pet form stool that’s not too hard and not too soft.

Some of the healthy sources of fiber commonly found in pet foods include beet pulp, oats, barley, peas, wheat bran, potatoes, apples, carrots, and pumpkin. If your pet suffers from either diarrhea or constipation, a little extra fiber can help. Inulin and psyllium are two fibers you can add (gradually) to your pet’s diet to help with stool consistency. And since they’re also prebiotics, these particular fibers help by providing food for beneficial gut microbes as well.

What about Probiotic and Prebiotic Supplements?


Probiotic supplements contain viable microorganisms (such as Lactobacillus and Bifidobacteria), but most commercially available probiotics — even the ones marketed for pets — don’t contain the particular kinds of microbes your dog needs. Such bacterial probiotics can sometimes improve symptoms temporarily, but the bacteria they contain are unlikely to take up permanent residence in your dog’s & cat's digestive system, so these products can’t do much to correct an imbalance.

However, there’s one probiotic supplement we do recommend. Saccharomyces boulardii is a probiotic yeast that has been extensively studied for its ability to promote digestive health, as documented in over 250 peer-reviewed articles to date. This particular probiotic has been shown to be particularly effective at resolving diarrhea caused by antibiotics. In a study of dogs with chronic intestinal disease, adding S. boulardii to the standard treatment (which included an antibiotic) resolved diarrhea within five days.


Prebiotics are specific substances — such as inulin, fructooligosaccharides (FOS), mannan oligosaccharide (MOS), and certain other sources of fiber — that promote the growth of healthy gut microbes. Although many pet foods naturally contain these ingredients, supplementing your dog’s diet with extra prebiotics can be a helpful option. Studies in mice have shown that by shifting the composition of the microbiome, prebiotics can counteract the inflammatory effects of a high-fat diet. 

Although prebiotics provide a useful tool to shift the microbiome, in large amounts such supplements could also unintentionally promote the growth of unwanted bacteria. If you want to try prebiotic supplements, start with small doses to see how your dog responds.

If your dog’s microbiome imbalance is moderate to severe, dietary changes and prebiotics may not be enough. In these cases, a fecal microbiota transplant (FMT) may help. A growing body of research has found that fecal transplants can help improve several different gastrointestinal disorders (as well as many other conditions) by changing the gut microbiome.

What Is a Fecal Microbiota Transplant (FMT)?

A fecal microbiota transplant (FMT), also called a fecal transplant, is the transfer of stool from a healthy donor to the GI tract of a sick recipient. The stool from the donor contains a diverse, well-functioning community of gut microbiota (including thousands of different kinds of healthy species-appropriate bacteria) that take up residence in the recipient’s gut. FMT has been used in veterinary medicine since at least the 17th century and in human medicine for thousands of years. It is one of the best approaches for restoring a balanced gut microbiome and is proven as an effective treatment in both humans and animals.

In cats & dogs, an FMT can be delivered in a veterinary clinic via colonoscopy, enema, or endoscopy. Those procedures generally require sedation and can be costly for pet parents. Our KittyBiome™ and DoggyBiome™ Gut Restore Supplement is an oral FMT capsule that gives your pet the benefits of FMT without the need for surgery or sedation. The Gut Restore Supplements (aka “poop pills”) deliver viable bacterial cells native to cats in a proprietary mixture of carefully screened, cryoprotected, freeze-dried donor stool. Our FMT capsules offer a noninvasive, affordable, at-home alternative for pets.

*Note that Gut Restore Supplement is currently not available in Singapore.

How Can Fecal Microbiota Transplant Improve Your Pet’s Health?

By seeding your cat’s & dog's gut microbiome with all the right bacteria and other microbes in the right proportions, a fecal transplant can help reestablish balance and resolve symptoms caused by an imbalanced gut. A fecal transplant can fill in any missing types of important beneficial bacteria, reduce harmful bacteria, and increase diversity in your pet’s gut. And a diverse, balanced gut microbiome helps keep your cat and dog healthy in multiple ways, by supporting their digestion, immune function, skin health, cognitive functions, and more.

How Do the KittyBiome & DoggyBiome Gut Restore Supplements (FMT capsules) Work?

  • Add Good Bacteria

When cats and dogs with digestive symptoms, skin issues, or immune system problems turn out to be missing certain groups of important gut bacteria, we need to add those missing members to the gut microbiome. 

Unlike probiotics, our KittyBiome DoggyBiome Gut Restore Supplement provides a whole community of thousands of different kinds of bacteria and other microbes that are native to healthy cats & dogs. The capsule’s enteric coating prevents it from dissolving until it reaches the intestines, where the contents seed your cat’s and dog's gut with a diverse array of healthy “good” bacteria, restoring any missing groups.

  • Reduce Harmful Bacteria

If your pet’s gut microbiome is out of balance because of an overgrowth of harmful bacteria, restoring balance will require reducing or removing those troublemaking groups.

One way to remove harmful bacteria from the mix is through competitive exclusion via fecal transplant. When we provide the beneficial gut bacteria with plenty of the food they like to eat, they thrive and multiply. Their greater numbers then take up more of the available resources, leaving less for the harmful bacteria. Through this process, beneficial members of the gut can keep harmful members in check or even cause those “bad” bacteria populations to gradually shrink and die out. In human healthcare, for example, that’s how FMT works against C. difficile infections.

What Are Bacteriophages?

Sometimes competitive exclusion on its own can’t win control back from the harmful bacteria (pathogens) that are contributing to your cat’s symptoms. In these cases, fecal transplant is much more likely to have a positive result if we first knock out particular harmful bacteria with more targeted therapies, such as bacteriophages.

Bacteriophages (or phages for short) are “friendly” viruses that attack specific types of bacteria. Our GMP product contains a phage cocktail called PreforPro that resolves diarrhea by reducing harmful levels of E. coli or C. diff. A powerful blend of phages, prebiotics, and probiotics, GMP stops occasional cat & dog diarrhea flare-ups, taking harmful bacteria out of the mix so the beneficial bacteria in your pet’s microbiome have more room to grow.

  • Increase Diversity

Our FMT capsules provide a diverse community of healthy cat and dog-specific bacteria, providing all the right types of bacteria in the right proportions. Diversity is important because each type of bacteria has a specific job to do to support the health of the body. The KittyBiome & DoggyBiome Gut Restore Supplements help resolve symptoms by giving your cat’s & dog's gut microbiome all the important members it needs to function well.

Your cart is currently empty.
Continue shopping