Maintain the Microbiome

How to Improve and Maintain Your Cat's or Dog's Gut Health

Your pet’s gut microbiome—made up of billions of beneficial bacteria and other microbes that live in the gastrointestinal (GI) tract—is a complex, constantly changing ecosystem. The composition and behavior of the gut’s microbial community are influenced by a lot of factors, including age, diet, environment, and medications.

Some factors—like illness, parasite infections, genetic predisposition, and antibiotics—can interfere with the proper functioning of your pet’s microbiome, leading to troublesome symptoms like diarrhea, vomiting, bloating, constipation, or itchy skin. But the good news is that we can use other factors, like diet and supplements, to help the gut microbiome stay strong and healthy. Here are some ways to support and maintain a healthy gut.

Feed a Healthy, Balanced Diet

A healthy diet is the best way to manage the gut microbiome. Since the bacteria that live in the gut help digest your pet’s food, what you feed your cat or dog influences which groups of gut bacteria thrive and multiply. For example, some commercially available pet diets are highly processed foods that contain a lot of carbohydrates, which encourage the growth of particular groups of gut bacteria that love carbs. When these bacteria multiply too successfully, they can crowd out other important bacteria groups, reducing diversity in the microbiome. And some carb-loving bacteria groups are associated with excessive inflammation, which can cause a variety of problems throughout the body.

Cats are obligate carnivores, so their gut microbiomes function best on a diet that’s high in protein (containing more than 40% protein on a dry-matter basis) and low in carbohydrates. Dogs are carnivores too, though in living closely with humans over thousands of years, they’ve developed the ability to metabolize a wider variety of foods. A balanced dog diet should be more than 35% protein on a dry-matter basis, should be low in fat, and should include healthy whole grains and other nutritious elements, such as fermented foods.

Include Fermented Foods

Fermented foods are considered probiotic foods because they contain “friendly” varieties of live bacteria. Since many groups of beneficial bacteria are produced by the fermentation process, fermented foods are an especially good source of these healthy microbes. Your own diet may already include some of these foods, such as yogurt, kefir, miso, kimchi, kombucha, and sauerkraut. A few of these foods are safe and healthy for pets as well.

Your cat or dog can benefit from fermented foods like goat milk or yogurt

Your cat or dog can benefit from small quantities of yogurt or fermented goat milk, as long as it’s unflavored and doesn’t contain any artificial sweeteners (which can be harmful to animals). For cats, a teaspoon or two of yogurt or goat milk is plenty. Your dog can even have a little sauerkraut, as long as it’s low in salt.

As with any new addition to your pet’s diet, introduce fermented foods very gradually over 7–10 days to avoid digestive upset.

Test Your Pet’s Gut Health

Regular assessments of your pet’s gut microbiome can help you keep up with any changes before they lead to symptoms. For healthy cats and dogs, a Gut Health Test once a year—and after any antibiotic use—can tell you whether you need to adjust your pet’s diet, as well as which foods or supplements might be most helpful. If your cat or dog has chronic health issues, like IBD or diabetes, more frequent microbiome testing can give you the information you need to help them live longer, happier lives.

Understand Your Pet's Health From the Inside Out

Add Prebiotics, Probiotics, and Postbiotics

One way you can help promote the healthy bacteria in your pet’s digestive tract is by supplementing your cat’s or dog’s diet with prebiotics, probiotics, and postbiotics.


Prebiotics are particular sources of dietary fiber that provide food for beneficial gut bacteria. Different bacteria eat different things, so by feeding the right prebiotics, you can encourage the kinds of gut bacteria that will promote your pet’s digestive health and overall wellness. Prebiotics have also been found to help counteract the inflammation caused by a high-fat diet.

Inulin is one prebiotic fiber that’s easy to add to your pet’s food (starting with small amounts). Another is mannan oligosaccharides (MOS), a prebiotic derived from yeast cells that has been shown to improve intestinal health. Fructooligosaccharides (FOS)—chains of sugars found in soybeans, Jerusalem artichokes, and asparagus—provide food for certain beneficial gut bacteria. FOS has the advantage of being especially palatable to cats and dogs.


Microorganisms (usually bacteria) that are consumed for their health benefits are called probiotics. Some probiotic products marketed for cats and dogs may temporarily improve diarrhea, but the bacteria they contain can’t rebalance a disrupted microbiome. That’s because even the leading probiotic products tend to contain large quantities of just a few kinds of bacteria, and usually not ones that are native to cats or dogs. For example, Lactobacillus is a probiotic that supports human health by promoting beneficial gut flora (“good bacteria”)—and that has been shown to improve the symptoms of irritable bowel syndrome in humans—but it doesn’t do the same thing for cats and dogs.

Saccharomyces boulardii is a “friendly” strain of yeast that has been extensively studied for its probiotic effects, documented now in over 250 peer-reviewed articles. This particular probiotic has been shown to resolve diarrhea caused by antibiotics. In a study of dogs with chronic intestinal disease, adding S. boulardii to the standard treatment resolved diarrhea within five days.


When gut bacteria feed on prebiotics, they break down those prebiotic fiber molecules through a process of fermentation. And that fermentation activity produces waste products, or byproducts, which are referred to as postbiotics. Certain postbiotics have been found to support good gut health in several ways, especially by helping to reduce inflammation.

Learn more about cat and dog prebiotics, postbiotics, and postbiotics here.

Avoid Unnecessary Antibiotics

In some situations, antibiotics can be a valuable, even life-saving treatment. If your pet has a serious infection or an overgrowth of harmful bacteria, a course of antibiotics may be absolutely necessary. But because these drugs tend to kill a lot of beneficial bacteria along with the “bad bacteria,” antibiotics can make drastic, long-term changes in your pet’s gut microbiome.

So if your veterinarian recommends a course of antibiotics, it’s important to ask questions, including which particular bacteria the proposed antibiotic has been shown to work against and whether there are any alternative treatment options to consider.

If your cat or dog does need antibiotics, there’s still a lot you can do to help them feel better during and after treatment. Because antibiotics disrupt the normal functioning of the gut microbiome, diarrhea is a common side effect. AnimalBiome’s Gut Maintenance Plus supplement was specifically designed to help resolve flare-ups of diarrhea caused by antibiotics.

Gut Maintenance Plus contains both the probiotic S. boulardii—a species of yeast (so it’s not killed off by antibiotics)—and FOS, a prebiotic that S. boulardii likes to eat. A substantial body of research has demonstrated that S. boulardii resolves diarrhea caused by antibiotics, and FOS has been shown to work together with S. boulardii to improve intestinal health.

Other Ways to Improve Gut Health

The gut microbiome interacts with the body’s other systems in multiple ways, including the gut–brain axis, the system of chemical signals that allows constant communication between the gut and the central nervous system. That’s why the gut microbiome is involved in functions like mental health and cognition as well as digestion and metabolism. And while the gut affects all those different systems, those systems also affect the gut.

One of the reasons exercise is so good for your overall health—and that of your pet—is that it’s good for the gut microbiome. Studies have shown that exercise promotes the growth of various kinds of beneficial gut bacteria, including those that have anti-inflammatory effects and those that produce short-chain fatty acids (SCFAs), which are crucial for a healthy digestive system and are also involved in weight loss. High blood sugar and obesity are associated with gut microbiome dysfunction, but a strong, diverse community of gut bacteria processes glucose efficiently and helps the body maintain a healthy weight.

How To Improve Dog Gut Health
How To Improve Cat Gut Health

Sleep is also important for gut health. Researchers have found that good-quality sleep promotes greater diversity in the gut microbiome, which in turn supports the healthy functioning of the brain and immune system. In humans, getting enough sleep also promotes healthy digestion by lowering stress levels.

Extra Help for Older Pets and Pets with Chronic Health Conditions

If your pet is older or has a chronic health condition, daily supplementation with prebiotics or postbiotics can help the gut microbiome maintain its healthy balance.

We know that as cats and dogs age, their microbiomes change. We also know that certain health issues can keep an animal’s gut microbiota permanently out of balance. Many kinds of cancer, for example, disrupt the gut microbiome. Genetic factors may also affect the gut’s microbial balance. For example, some Boxers have a genetic predisposition that disrupts the proper functioning of the microbiome. In such cases, FMT capsules can help minimize symptoms, so Gut Restore Supplements may be an ongoing element of your pet’s care.

Ongoing microbiome support is especially important for pets with chronic digestive disorders. For example, if your cat or dog has inflammatory bowel disease (IBD), some steps you can take to manage their symptoms and help them feel better include gut health assessments, prebiotic/probiotic supplements, and vitamin B12 injections. Repeated courses of Gut Restore FMT capsules and/or Gut Maintenance Plus (GMP) can also help.

To Healthy & Happy Pets

To Healthy & Happy

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