10 Ways to Shape Your Dog’s Gut Health & Digestion

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Your dog has a unique collection of hundreds of different types of single-celled microorganisms (bacteria and other microbes) in its digestive tract, referred to as the gut microbiome. Gut bacteria are crucial for digestion and obtaining nutrients from the food your dog eats. From weight to mental health, the microbiome affects almost every aspect of your dog’s health and happiness.

When gut bacteria are out of balance, disorders such as inflammatory bowel disease (IBD) can result. Modern society is seeing a rise in microbiome-associated disorders in our dogs and ourselves. It’s more important now than ever to take care of our dogs’ microbiomes. But how do we do this?

How to take care of your dog’s microbiome

The advice you receive will vary, and that’s in part because the correct answer depends on what condition your dog’s microbiome is in. 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:

1. Microbiome condition: IF your dog does not have a wide variety of healthy gut microbes

Response: Add new microbes to your dog’s microbiome

2. Microbiome condition: IF your dog has an infection or overgrowth of harmful microbes

Response: Remove microbes from your dog’s microbiome

3. Microbiome condition: IF your dog has a diverse gut community but suffers from an imbalance

Response: Change the proportions of microbes that are already in your dog’s gut


I’ve put together a list of 10 factors that can shape your dog’s (and your) gut bacteria. Read on as I discuss their uses.

Reveille dog - AnimalBiome
10 Ways to Shape Your Dog’s Gut Health & Digestion

Adding new microbes to your dog’s microbiome

This post is especially useful for dogs whose gut microbiomes lack sufficient diversity in the bacteria that are present. Your dog's gut microbiome might have low diversity if it was recently prescribed antibiotics, or if it has been exposed to a disease-causing pathogen. However, keep in mind that very few bacteria will survive the journey through your dog’s stomach to the large intestine (where the gut microbiome is located). AnimalBiome does not currently have scientific evidence that 1-4 can change the gut microbiomes of adult dogs.

Here are five sources of new microbes for your dog:

1)    Fresh air and nature

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.

dog looking across mountain - AnimalBiome
‍Bacteria that are potentially good for your dog are everywhere in nature

2)    Raw foods

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

3)    Good influences (you and your dog’s friends)

Let’s face it: we share microbes with our dogs. 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).

4)    Probiotics and fermented foods

Many dog owners enjoy feeding their dogs probiotics and fermented foods that contain high quantities of live microbes. However, these probiotic microbes generally do not become permanent residents in your dog’s microbiome, which is why many probiotic users find the most benefit from daily supplementation.

5)    Fecal microbiota transplants (FMT)

Fecal microbiota transplants move the gut microbes from a healthy dog to a suffering dog. Fecal microbiota transplants 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 FMT capsules that make this process a little easier to swallow.

greyhound dog - AnimalBiome
AnimalBiome makes fecal microbiota transplants easier to swallow

Removing microbes from your dog’s microbiome

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

The following two approaches combat harmful microbes:

6)    Antibiotics

This is a very common treatment for both people and dogs. Antibiotics kill their targets by inhibiting essential life functions of pathogenic bacteria. However, most of these 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, you should also consider supporting your dog's microbiome (see #1-5 above) during and after treatment.

7)    Competing microbes

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. 

Chihuahua dog - AnimalBiome
When combating harmful bacteria, antibiotics is not the only answer

Changing the proportions of microbes that are already in your dog’s gut

Sometimes your dog might have a wide range of different types of gut microbes, but they are out of balance.

Here are three factors that influence the balance of bacteria in your dog’s gut:

8)    Diet

Because gut bacteria help your dog digest food, the types of food your dog eats will influence which bacteria thrive in the gut. For instance, in a study where dogs were fed a high-protein, low-fat diet, the microbiome balance of overweight dogs shifted to a balance associated with healthy weight.

9)    Prebiotics

Prebiotics are substances (typically fiber) that are consumed with the intent to promote the growth of healthy gut microbes. Although many 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 can shift the microbiome, they could also unintentionally promote the growth of harmful bacteria. If you want to try prebiotics, start with small doses to see how your dog responds. 

10)    Mental state

Gut bacteria can influence your dog’s mood, and it turns out that moods can also influence your dog’s microbiome. Stress has been shown to shift the microbiome of humans and squirrels towards a less healthy state. If your dog already suffers from digestive issues, this might explain why stress often worsens the symptoms. There are many techniques available to relieve stressed out dogs, and increased exercise is one of the most common recommendations.

corgi dog - AnimalBiome
Stress and mood changes can influence your dog's microbiome

Understand your dog’s gut health with an assessment

Knowing the composition of your dog’s microbiome will help you choose the best interventions for your dog. If you properly address your dog’s low gut diversity or imbalance, it could help prevent disorders like inflammatory bowel disease in the future. Our simple microbiome assessments will show you what types and proportions of bacteria are in your dog’s gut. We also provide online comparisons of your dog’s microbiome to other dogs so that you can decide if your dog’s microbiome needs an intervention.

Learn more about our assessment kits for dogs or cats.