Dog Gut Health: The 4 Ways to Restore It Naturally

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Your dog has a unique collection of hundreds of different types of bacteria and other microbes (such as viruses, fungi, etc) in its gastrointestinal tract (GI Tract), referred to collectively as the gut microbiome. A healthy microbiome is crucial for your dog’s overall health, from nutrient absorption to mental health. When bacteria become out of balance, disorders such as inflammatory bowel disease (IBD), digestive issues, immune system reactions, diabetes, and even depression can result.

Modern society is seeing a rise in microbiome-associated disorders in our dogs and ourselves. This is due to modern pet food diets, medications (particularly antibiotics), and lifestyle choices (ie. being mostly indoors, antimicrobial cleaners, etc).  Luckily, it is possible to restore and maintain a healthy gut microbiome for your pup without using medications with adverse side effects. In fact, it’s as simple as Test, Add, Remove, and Rebalance


The first step towards achieving a balanced diverse microbiome is to know the state of your dog’s intestinal health. The best way to do this is with a microbiome Gut Health Test - a process where you send in your dog’s poop to sequence the bacterial DNA in it (click here to learn more). The results will tell you what bacteria are present and in what amounts. By comparing your dog’s test results to those of healthy dogs of similar age and breed, the gut health test report provides an easy and affordable way to gain a detailed understanding of what changes may be necessary to improve your dog’s gut flora.

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

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

These conditions are connected to each other, and the solution for one condition may also help for the others. Therefore, we recommend reading each of the “Add”, “Remove”, and “Rebalance” sections to resolve any imbalances in your dog’s digestive tract. 


This step is especially useful for dogs whose gut microbiomes lack sufficient diversity or enough different kinds of bacteria. Your dog's gut microbiome might have low diversity if she or he was recently prescribed antibiotics, or has been exposed to a disease-causing pathogen such as E. coli or Salmonella. There are many ways to add good bacteria to your dog’s digestive system, and some methods are dependent on whether you are targeting your dog’s small intestine or large intestine

Diet: Are you feeding all of your dog’s microbes?

Diversity is a good thing! When it comes to your dog’s microbiome, bacterial diversity comes from the food your dog eats. From live bacteria to nutrients that allow good bacteria to flourish, there are many great ways to supplement your dog’s diet to improve their digestive health: 

  • Prebiotics. Prebiotics are substances, such as inulin, mannan oligosaccharide, and other sources of fiber that are consumed with the intent to promote the growth of healthy gut microbes. Although many pet foods naturally contain these ingredients, some people supplement their dogs’ diets with extra prebiotics. In mice, it has been observed that the microbiome shift induced by prebiotics can counteract the inflammatory nature of a high-fat diet. Although prebiotics provide a helpful tool to shift the microbiome, they could also unintentionally promote the growth of unwanted bacteria. If you want to try prebiotics, start with small doses to see how your dog responds. 

  • Fermented Foods. Not only can you feed your pet fermented food, it’s great for them! Sauerkraut, kimchi, yogurt, kefir, apple cider vinegar, tempeh, and MSG-free miso are all safe to feed your dog. There are many easy fermented vegetable recipes online just for dogs, such as those listed here

  • Raw Food. Raw fresh foods provide a source of natural microbes for your dog. Many people even feed their dogs raw meat diets, although you will need to follow appropriate safety precautions for handling meat if you want to try this for your dog. As you are aware, not all microbes that grow on food are healthy.

Fecal microbiota transplants (FMT)

Fecal microbiota transplants involve the transfer of fecal material (including good bacteria and fungi) from a healthy donor to the GI tract of a sick dog. FMTs are more powerful than probiotics because they help to reseed the gut with an entire ecosystem of beneficial bacteria that comes from dogs (most probiotics for dogs don’t come from dogs).  FMTs via enema are typically performed in a veterinary hospital under sedation, often making them costly and stressful for the dog. At AnimalBiome we offer oral Gut Restore (fecal transplant) capsules that make this process a little easier to swallow at fractions of the cost.

How can I improve my dog's gut health?
AnimalBiome makes fecal microbiota transplants easier to swallow.

Environmental Exposure 

Getting fresh air and being out in nature come with numerous health benefits, including some lesser known positive impacts on pet 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 microbes elsewhere too. Research shows that humans and their dogs share skin bacteria. Your dog’s furry playmates probably share their microbes as well. Your dog may even be coprophagic (poop-eater). All of this exposure to a diversity of microflora accumulate to strong intestinal health and immune health.

Tips for improving dog gut health, good bacteria is in nature- AnimalBiome
Bacteria that are potentially good for your dog are everywhere in nature.


Not all microbes are helpful members of your dog’s gut community. Sometimes your dog might have an infection or overgrowth of harmful microbes (“bad bacteria”) that requires an intervention.

Out-Compete Bad Bacteria

Although it may seem counterintuitive to add microbes in order to remove other microbes, this can be a surprisingly effective treatment. For instance, when humans have antibiotic-resistant C. diff infections, fecal transplants are used to deliver new microbes to the patient’s gut that compete with and kill off C. diff. Although FMTs have been shown to be very effective at treating C. diff infections in people, this potentially life-saving treatment is often used as a last resort. Fecal transplants have 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 to treat an infection caused by pathogenic bacteria. Most antibiotics are "broad-spectrum" antibiotics, meaning that when they kill the harmful bacteria, they take out the beneficial bacteria as well. Antibiotics deplete the microbiome and can cause long-term changes to your dog's microbiome. If your dog needs to take antibiotics, it is important that you support and restore your dog’s loss of gut bacteria both during and after treatment by following the advice in the “Add” section above. It is important to do a microbiome test of your dog’s gut health after antibiotic treatment to help guide your choices for a fast recovery. 


Bacteriophages, or ‘phages’ for short, are tiny viruses that infect bacteria. Phage therapy is the process of introducing phages that specifically target bad bacteria. The technology has been around for a century, but has resurfaced due to the decline in global effectiveness of antibiotics. Luckily, there is a safe phage therapy available for humans and animals alike who have high levels of E. coli, which happens to be one of the most common bacterial overgrowth issues observed in dog guts. Gut Maintenance Plus capsules contain four different phages that kill E. coli, in addition to other beneficial ingredients for gut health. 

How do you treat leaky gut in dogs?
When combating harmful bacteria, antibiotics are not the only answer.


Sometimes your dog might have a wide range of different types of gut microbes, but they are out of balance. There are several ways to restore this balance with diet or a dog gut health supplement:

Diet is the Primary Way to Manage Your Dog’s Microbiome

Good nutrition is one of the cornerstones for 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 dog’s microbiome, and each kind requires certain nutrients to survive. Therefore, the food your dog eats will influence which bacteria thrive in the gut.

For example, many kibble diets are too high in carbohydrates, which doesn’t promote the growth of all beneficial bacteria. In a study where dogs were fed a high-protein, low-fat dog food, the microbiome balance of overweight dogs shifted to a balance associated with healthy weight. Use this calculator to find the hidden amount of carbohydrates and make sure your dog’s food has more than 50% protein on a “dry matter” basis.  

If the nutrition in your dog’s diet is balanced, yet he or she still has symptoms of digestive health issues, it is possible that a food intolerance or allergy is to blame. Food sensitivities are quite common, and can be resolved with changing your dog’s food. It is important to talk to your veterinarian before changing your dog’s diet, as some have been linked with certain health issues. Lastly, it’s important to remember, “grain-free” and “gluten-free” diets can still contain high levels of carbohydrates. 

A healthy, balanced dog diet with good nutrition is the primary way to manage your dog's gut health.
Diet is the primary way to manage your dog's gut health.

Test, Add, Remove, and Rebalance

All aspects of your dog’s health are connected to his or her gut microbiome in some way. In this article we discussed the importance of testing your dog’s microbiome composition to help you choose the best interventions for your dog. Microbiome testing will help you make productive choices for your pet’s health and allow you to address low diversity and/or imbalances early to help prevent numerous disorders such as inflammatory bowel disease, diabetes, and obesity. This article outlines natural ways to add, remove, and change the presence and balance of microbes in your dog’s gut. Please visit AnimalBiome’s page to learn more about testing, the importance of the microbiome, and how AnimalBiome can help your furry friends. 

This article was originally published on 10/3/18. It was updated on 11/20/20. If you liked this article, please consider sharing it.