Restore Your Dog’s Microbiome

How to Restore and Improve Your Dog’s Gut Health

If your dog 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 dogs’ symptoms do improve in response to dietary changes or medication, other dogs 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 dog 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 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 gut microbiome, leading to worrisome symptoms like diarrhea, constipation, bloating, weight loss, obesity, or itchy skin.

In many cases, 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 dog 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 Dog’s Gut Health?

If your 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 dog’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: Missing good bacteria

Possible Causes: Age, Genetics, Diet, Parasites, Pathogens, Antibiotics

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

Microbiome Condition: Too many harmful bacteria

Possible Causes: Diet (e.g., too much carbohydrate), Infection, Illness

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

Microbiome Condition: Right bacteria, wrong proportions

Possible Causes: Age, Diet (e.g., not enough fiber from vegetables, fruits, and whole grains)

Response: Rebalance your dog’s gut bacterial populations with dietary changes and prebiotics.

Your Dog’s Diet Impacts Their Gut Health

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

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

Feed Enough Protein

Despite their long association with humans, dogs are still more carnivore than true omnivore, so they need a diet that’s high in protein and low in carbohydrates. Adding more protein to your dog’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 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 food. It is important to talk to your veterinarian before changing your dog’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 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. 

The food you choose for your dog should contain at least 35% protein 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 dog’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 dogs. The kinds of bacteria found in goat milk and other fermented foods can help maintain a healthy dog’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 dog’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 dog’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 dog’s blood glucose at a healthy level. Insoluble fiber holds on to moisture and helps your dog form stool that’s not too hard and not too soft.

Some of the healthy sources of fiber commonly found in dog foods include beet pulp, oats, barley, peas, wheat bran, potatoes, apples, carrots, and pumpkin. If your dog suffers from either diarrhea or constipation, a little extra fiber can help. Inulin and psyllium are two fibers you can add (gradually) to your dog’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 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 dog 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 animals and humans.

In 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 dog parents. Our DoggyBiome™ Gut Restore Supplement is an oral FMT capsule that gives your dog the benefits of FMT without the need for surgery or sedation. The Gut Restore Supplements (aka “poop pills”) deliver viable bacterial cells native to dogs in a proprietary mixture of carefully screened, cryoprotected, freeze-dried donor stool. Our FMT capsules offer a noninvasive, affordable, at-home alternative for dogs.

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

By seeding your 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 dog’s gut. And a diverse, balanced gut microbiome helps keep your dog healthy in multiple ways, by supporting their digestion, immune function, skin health, cognitive functions, and more.

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

Add Good Bacteria

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

Reduce Harmful Bacteria

If your dog’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 dog’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 DoggyBiome™ 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 dog diarrhea flare-ups, taking harmful bacteria out of the mix so the beneficial bacteria in your dog’s microbiome have more room to grow.

Increase Diversity

Our FMT capsules provide a diverse community of healthy 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 DoggyBiome Gut Restore Supplements help resolve symptoms by giving your dog’s gut microbiome all the important members it needs to function well.

“So far we’ve had great success

about DoggyBiome™ GMP
Bill 05/13/22

“This product has worked better than any other for the management of diarrhea. I’ve used it on several different dogs with the same outcome each time. Diarrhea resolves and firm stools return. I will always keep a reserve supply on hand.”

“Noticeable improvement in diarrhea frequency/severity.

“My dog has had chronic diarrhea for years and would often wake me up in the middle of the night during the worst bouts to relieve itself. The fur cleanup was always a huge mess and I’m sure it was not doing any favours to my dog’s health. Since having her undergo a course of Gut Restore Supplement and Gut Maintenance treatment, followed by maintenance doses of the S. boulardii + FOS powder, she rarely has diarrhea and I’ve had zero awakenings in the middle of the night to toilet. These products were well worth the investment for my dog’s health and well-being in addition to my own quality of life caring for her.”

A solution that worked

“We tried everything for our 4 year old Golden Retriever and this was the only thing that fixed his GI issues. We are so grateful we found it!”

Gut Restore Works!

“My dog went from 5 liquid poops a day to two formed poops a day after taking Gut Restore. I saw an improvement in her poops after a few doses! I have tried so many other products. None worked. My vet was even suggesting that I put my dog on long term Flagyl. So happy I found this site and their products! Plus they have excellent customer service as I called or emailed them a few times. I highly recommend this product!”

The solution to a healthy dog’s gut!

“I have tried EVERYTHING to clear up my pitbull’s skin and nothing has worked until now. This is exactly what her gut needed and it has made her coat shine like never before. We are thrilled. I’m excited to see how long it takes for it to seed and she naturally produces the healthy bacteria.”


“The change in 30 days is incredible, healthy skin, normal poop. We hope to see the result of the next test.”