Restore the Microbiome

Rebalance the Microbiome: How to Improve Your Patient’s Gut Health

If your patient 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 cats’ and dogs’ 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 patient 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 patient 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 patient’s gut microbiome, leading to worrisome symptoms like diarrhea, constipation, bloating, weight loss, obesity, or itchy skin.

In many cases, cats and dogs 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 patient needs aren’t present in the right numbers, the microbiome is out of balance. As a result, some of the gut’s important functions stop working, leading to a variety of uncomfortable symptoms.

Luckily, even in cases of serious imbalance, it is possible to restore the microbiome to a healthier state.

What Can I Do to Restore My Patient’s Gut Microbiome?

If your cat or dog 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 patient’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:

Microbiome Condition Possible Causes Response

Some important bacterial groups are missing.

age, genetics, diet, parasites, pathogens, antibiotics

Add new bacteria to your patient’s microbiome via dietary changes or fecal microbiota transplant (FMT).

Populations of harmful bacteria have become too large.

diet (e.g., too much carbohydrate), infection, illness

Reduce or remove overgrown harmful bacteria with bacteriophages or by “competitive exclusion” via FMT.

All the important bacteria are there, but not in the right numbers.

age, diet (e.g., too many carbohydrates or not enough fiber from vegetables, fruits, and whole grains)

Rebalance your patient’s gut bacterial populations with dietary changes and prebiotics.


Diet is the primary way to manage your patient'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 hundreds of different kinds of gut bacteria in your patient’s microbiome, and each kind requires certain nutrients to survive. Therefore, the food your patient eats will influence which groups of bacteria thrive in the gut. Simple changes to your patient’s diet might be enough to restore balance.

Things to Consider When Thinking About Your Patient’s Diet

Feed Enough Protein

Cats are obligate carnivores, and dogs, despite their longer association with humans, are still more carnivore than true omnivore, so both need a diet that’s high in protein and low in carbohydrates. Adding more protein to your patient’s diet also supports the growth of the important Fusobacteria group, which do best in a high-protein environment.

If your patient is fed a diet that is nutritionally well balanced and 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 patient’s food. It is important to talk to your veterinarian before changing your patient’s diet, as some diets have been linked with certain health issues.

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 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.

The food you suggest for feline patients should have at least 40% protein on a “dry matter” basis; for canine patients, make sure the dry-matter protein content is at least 35%. 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 patient’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 cats and dogs. 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 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 chronic oxidative stress–related diseases (such as glaucoma, cancer, Parkinson’s, and Alzheimer’s). Consider the ingredients included in your patient’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 patient’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 patient’s blood glucose at a healthy level. Insoluble fiber holds on to moisture and helps your patient 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 patient suffers from either diarrhea or constipation, a little extra fiber can help. Inulin and psyllium are two fibers you can add (gradually) to your patient’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.

Feed Raw Foods (Safely)

Fresh raw foods—such as unpasteurized milk, raw meat, and uncooked vegetables—are sources of naturally occurring microbes for your patient. Many people feed their pets high-quality raw meat diets. When preparing such diets at home, always follow appropriate safety and hygiene practices for handling raw meat and dairy products.

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 patient needs. Such bacterial probiotics can sometimes improve symptoms temporarily, but the microbes they contain are unlikely to take up permanent residence in your patient’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 patient’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 patient responds.

If your patient’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 bacteria) that take up residence in the recipient’s gut. FMT has been used in human medicine for thousands of years and in veterinary medicine since at least the 17th century. It is the best known approach for restoring a balanced gut microbiome, and it has proven to be an effective treatment in both humans and animals.

An FMT can be delivered via colonoscopy or enema, but for cats and dogs, those procedures generally require sedation. Our Gut Restore Supplement is an oral FMT capsule that gives your patient the benefits of FMT without the need for surgery or sedation. Containing a proprietary mixture of carefully screened, cryoprotected, freeze-dried donor stool, the FMT capsules offer a noninvasive, affordable, at-home alternative for pets. Learn more about our FMT capsules.

How Can Fecal Microbiota Transplant Improve My Patient’s Health?

When pets 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 microbiome and help the new populations grow and thrive.

Fecal transplants introduce a whole community of healthy cat- or dog-specific microbes, seeding your patient’s gut with a diverse array of beneficial bacteria and filling in any missing groups.

If, instead of missing some bacterial groups, your patient’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.” 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 microbiome 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.

Sometimes competitive exclusion on its own can’t win control back from the pathogens that are contributing to your patient’s symptoms. In these cases, the introduction of an array of healthy gut microbes will be much more likely to have a positive result if we first knock out particular harmful bacteria with more targeted therapies, such as bacteriophages.

Bacteriophages are “friendly” viruses that attack specific types of bacteria. Some bacteriophages, for example, specifically target E. coli. Our Gut Maintenance Plus product contains a prebiotic bacteriophage cocktail called PreforPro, which helps take harmful bacteria out of the mix so the beneficial bacteria in your patient’s microbiome have more room to grow.

To Healthy & Happy