Dog Gut Health: The 4 Ways to Restore It Naturally

Your dog’s gastrointestinal tract (GI tract) hosts a unique collection of thousands of different types of bacteria, viruses, fungi, and other microorganisms, referred to collectively as the gut microbiome. A diverse, well-balanced gut microbiome is crucial for almost every aspect of your dog’s overall health, from nutrient absorption to cognitive functions. When the different populations of gut bacteria are out of balance, disorders such as inflammatory bowel disease (IBD), immune system reactions, and even depression can result.

Modern society is seeing a rise in microbiome-associated disorders in our dogs and ourselves. That’s due to a number of factors, including commercial pet diets, medications (particularly antibiotics), and lifestyle choices (being mostly indoors, using antimicrobial cleaners, etc.).

 Luckily, it’s possible to restore and maintain a healthy gut microbiome for your pup without using medications that can cause adverse side effects. In fact, it’s as simple as Test, Add, Remove, and Rebalance.

(1) Test

Many symptoms—like diarrhea, vomiting, constipation, itchy skin, and even bad breath—can actually be a sign of trouble in your dog’s gut microbiome. That’s because when important groups of bacteria are missing or out of balance, some of the gut’s important digestive and immune functions stop working. Microbiome testing is a great way of finding out what’s really going on in your dog’s gut.

How Does Microbiome Testing Work?

Gut microbiome testing means examining the bacteria and other microorganisms present in an individual stool sample. The bacteria in your dog’s poop provide a snapshot of their gut microbiome.

Our DoggyBiome Gut Health Test kit includes everything you need to collect a small sample of your dog’s poop and send it to our lab. We use DNA sequencing to identify all the different kinds of bacteria in your dog’s sample, so we can tell you what kinds of bacteria are present in your dog’s gut microbiome and in what proportions. (Learn more about microbiome testing.)

What’s in the Report?

You’ll receive a Gut Health Test report that clearly explains your dog’s individual results. By comparing your dog’s results to those of healthy dogs of similar age and breed, the report also helps you see what changes might be necessary to improve your dog’s gut health.

While many dogs start off life with a healthy mix of gut flora, this mix can change because of aging, illness, or exposure to certain medications, particularly antibiotics. The table below explains the three gut microbiome conditions your dog could suffer from and the appropriate responses. Any advice to shape your dog’s gut microbiome will fall into at least one of these three response categories:

Dog Microbiome Condition Chart: Add, Remove, or Rebalance Microbes

Dog Microbiome Condition and Response Chart

These three conditions are connected to each other, so the solution for one condition may also help the others. Therefore, we recommend reading all of the sections below to learn how the “Add,” “Remove,” and “Rebalance” approaches can help resolve any imbalances in your dog’s gut microbiome.

(2) Add

Adding beneficial bacteria is especially useful for dogs whose gut microbiomes lack sufficient diversity (enough different kinds of bacteria). A dog’s gut microbiome might have low diversity if they recently had a round of antibiotics or were exposed to a pathogen, such as E. coli or Salmonella. There are many ways to add good bacteria to your dog’s digestive system. Some methods are dependent on whether you are targeting your dog’s small intestine or large intestine.


Diet: Are You Feeding the Right Gut Bacteria?

Diversity is a good thing! When it comes to your dog’s gut microbiome, bacterial diversity starts with what your dog eats. Not only do the right foods help good bacteria flourish, but there are also many ways to supplement your dog’s diet to improve their digestive and overall health.


  • Prebiotics. Prebiotics are particular kinds of dietary fiber—such as inulin, mannan-oligosaccharides (MOS), and fructo-oligosaccharides (FOS)—that promote the growth of beneficial gut bacteria. Feeding the “good” bacteria in the digestive tract leads to all kinds of benefits, including strengthening your dog’s immune system. In mice, it has been observed that by shifting the gut microbiome, prebiotics can even counteract the inflammatory effects of a high-fat diet. If you want to try a prebiotic supplement, start with small amounts to see how your dog responds.

  • Probiotics. Most probiotic supplements marketed for dogs contain high quantities of a few specific strains of live bacteria. But the bacteria in these supplements typically aren’t strains that are native to dogs, so they won’t become permanent residents of your dog’s gut. While these products may provide temporary relief from symptoms like diarrhea, most probiotics for dogs won’t solve the underlying problem. One probiotic that’s been proven safe and effective in dogs is Saccharomyces boulardii. Rather than a type of bacteria, S. boulardii is a strain of yeast that is especially helpful for regrowing gut microorganism populations that have become imbalanced.

  • Fermented foods. Beneficial bacteria “eat” prebiotics through a process of fermentation, which produces a variety of health-promoting substances called postbiotics, including short-chain fatty acids (SCFAs). One big reason fermented foods are so good for us is that they contain a lot of those postbiotics, which play important roles in digestion, immune cell production, nervous system function, and many other aspects of the body’s health. Fermented foods are good for your dog too. Low-salt sauerkraut, unsweetened yogurt (be aware that some sugar-free yogurts contain artificial sweeteners that are harmful to dogs!), kefir, apple cider vinegar, tempeh, and MSG-free miso are all safe to feed your dog in small amounts. You can find easy fermented vegetable recipes online that are designed specifically for dogs, such as those listed here.

  • Whole foods. Fresh, plant-based ingredients are great for your dog’s gut health. Non-starchy, fibrous vegetables—like broccoli, green beans, carrots, cauliflower, asparagus, and leafy greens (like spinach, kale, or collards)—contain the kinds of prebiotic fiber that beneficial gut bacteria like to eat. These foods are also rich in antioxidants and are an important part of an anti-inflammatory diet.Pro tip: Adding prebiotics, probiotics, and postbiotics to your dog’s diet is easy with our safe, effective supplements designed specifically for dogs. The probiotic and prebiotic DoggyBiome S. boulardii + FOS Powder can be mixed into your dog’s food. Tasty DoggyBiome ImmuneShield chews contain a postbiotic formula designed to improve gut and immune health.


Environmental Exposure

Getting fresh air and being out in nature come with numerous health benefits, including some lesser-known positive impacts on gut health. Bacteria that are potentially good for your dog are everywhere in nature: in the dirt, on plants, and even in the air. Take your dog for a walk in nature or crack open a window and let in some fresh air.Your dog gets new microorganisms elsewhere too. Research shows that humans and their dogs share skin bacteria. Your dog’s furry playmates probably share their microorganisms as well. And if your dog is coprophagic (a poop eater), they may be ingesting microorganisms from other dogs’ gut microbiomes. All of this exposure to a diversity of microflora can contribute to strong intestinal and immune health.

(3) Remove

Not all microorganisms are helpful members of your dog’s gut community. An infection or overgrowth of harmful (“bad”) bacteria requires an intervention.


Although it may seem counterintuitive to add microorganisms in order to remove other microorganisms, this approach can be surprisingly effective. For instance, when humans have antibiotic-resistant C. difficile (C. diff) infections, FMT is used to deliver new bacteria to the patient’s gut that compete with and kill off C. diff.

When new populations of beneficial bacteria take nutrients and space away from the pathogenic (disease-causing) bacteria through successful competition, the “bad” bacterial populations shrink. FMT has proven to be just as effective in many animals, including dogs.


For many people, antibiotics aren’t considered “natural,” but your vet may strongly recommend them if your dog has an infection caused by pathogenic bacteria. Most of these medications are “broad-spectrum” antibiotics, meaning that they kill a lot of different kinds of bacteria—not just harmful bacteria but beneficial ones as well. Because antibiotics deplete the gut’s bacterial community, they can cause unhealthy long-term changes to your dog’s microbiome.

If your dog needs to take antibiotics, it’s important that you support and restore your dog’s gut health both during and after treatment by following the advice in the “Add” section, above. It’s also important to test your dog’s gut health after a course of any antibiotic to find out what changes the medication might have caused and what you can do to help your dog’s gut microbiome recover quickly.


Bacteriophages (the name means “bacteria eaters”)—or “phages” for short—are naturally occurring microorganisms that attack and kill particular kinds of bacteria. Phage therapy is the process of introducing phages that specifically target bad bacteria. This approach has been around for a century, but phages have gained new attention as an effective alternative to antibiotics as a result of the global decline in antibiotics’ effectiveness. (Learn more about the problem of antimicrobial resistance.)

Luckily, a safe phage therapy is available for humans and animals who have high levels of E. coli, which happens to be one of the most common gut microbiome imbalances observed in dogs. Our Gut Maintenance Plus capsules contain four different phages that kill E. coli, in addition to other beneficial prebiotics and probiotics for dogs that support and improve gut health.

(4) Rebalance

Sometimes a dog’s gut contains a healthy range of different types of gut microorganisms (good diversity), but the sizes of the different populations are out of balance. In such cases, dietary changes and/or gut health supplements can often restore a healthy balance.

Diet Is the Primary Way to Manage Your Dog’s Gut Health

Good nutrition is one of the cornerstones of overall health. It helps prevent common illnesses, boosts the immune system, and positively influences the gut microbiome. There are thousands of different kinds of bacteria in your dog’s gut microbiome, and each kind requires certain nutrients to survive. Therefore, what your dog eats will influence which bacteria thrive in their gut.


Dogs Need a High-Protein, Low-Carbohydrate Diet

For example, many kibble diets are too high in carbohydrates, so they don’t promote the growth of all the beneficial bacteria your dog needs. Carbohydrates feed the “bad” kinds of bacteria that increase inflammation, contribute to “leaky gut” syndrome, and promote weight gain.

Dogs are still carnivores, which means they (and their gut bacteria) do best on a diet that’s high in protein and low in carbohydrates. In a study where dogs were fed a high-protein, low-carbohydrate diet, the gut microbiome composition of overweight dogs shifted to the balanced bacterial proportions associated with healthy weight loss.

Use this calculator to find the hidden amount of carbohydrates in any pet food, and make sure your dog’s diet contains more than 50% protein on a “dry matter” basis. Remember that dog foods labeled “grain-free” and “gluten-free” can still contain high levels of carbohydrates, and may not be the best choice for their digestive health.


Don’t Forget Fiber!

Dietary fiber is important for improving the transit time of matter passing through the digestive tract and for feeding beneficial bacteria. It is easy to add fiber to your dog’s diet: you can do this by adding whole food or prebiotics, both of which are discussed above.


Food Intolerances and Food Allergies

If your dog is eating an appropriate, nutritious diet but still has symptoms of digestive issues (like diarrhea, constipation, or bloating), a food intolerance or allergy may be to blame. Food sensitivities (intolerances) are quite common and can usually be resolved by changing your dog’s food. It is important to talk to your veterinarian before changing your dog’s diet, as some commercial foods have been linked to certain health issues.



Fecal Microbiota Transplantation (FMT)

Fecal microbiota transplantation (FMT), or fecal transplant, is the transfer of fecal material (including beneficial bacteria and other microorganisms) from a healthy donor to the GI tract of a sick patient. For dogs with gut microbiome imbalances, FMT is more effective than probiotics because it helps reseed the gut with an entire ecosystem of dog-specific beneficial bacteria. (Most so-called dog probiotics don’t contain bacteria that come from dogs.)

FMT via enema is typically performed in a veterinary hospital under sedation, making this procedure costly for pet parents and stressful for dogs. Our DoggyBiome Gut Restore Supplement (FMT in an oral capsule) makes this approach easier to swallow at a fraction of the cost. Learn more about FMT.

Where to Start?

You may already recognize one or more simple changes you could make to improve your dog’s gut health. A little more protein or fermented food in their diet, a daily prebiotic supplement, or some regular outdoor exercise might be enough to boost your dog’s digestive and immune health.

If your dog is suffering from digestive symptoms or skin issues, or you’re just not sure whether Adding, Removing, or Rebalancing sounds like the right approach, a Gut Health Test can help. In addition to showing you what’s really going on in your dog’s gut microbiome, your test report will include personalized recommendations for dietary and lifestyle changes that can help your dog live a longer, healthier life.

Test, Add, Remove, and Rebalance

Almost every aspect of your dog’s health is connected to their gut microbiome in some way. Testing your dog’s gut microbiome composition can give you valuable clues about how various symptoms may be related to the state of your dog’s gut. By helping you choose the right interventions to address low diversity and/or imbalances early, microbiome testing can help improve or even prevent disorders like IBD, diabetes, and obesity.


Learn more about microbiome testing, the importance of the gut microbiome, and how AnimalBiome can help your dog.

Questions to Ask Your Veterinarian

Am I feeding my dog the right food?

Can I stop the antibiotics once my dog’s symptoms improve?

What symptoms are a sign that my dog has a gut microbiome imbalance?

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