Shopping Cart

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

Posted by Alex Martin on

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, inflammatory 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:

Microbiome condition:


IF your dog does not have a wide variety of healthy gut microbes

Add new microbes to your dog’s microbiome

IF your dog has an infection or overgrowth of harmful microbes

Remove microbes from your dog’s microbiome

IF your dog has a diverse gut community but suffers from an imbalance

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.

Adding new microbes to your dog’s microbiome

This response is especially useful for dogs that do not have as many different types of bacteria in their gut as healthy dogs. Your dog might have low diversity if it was raised in a sterile environment or has been prescribed antibiotics. 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.

2)    Raw foods

Raw fresh foods (like vegetables) 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), although this practice is undesirable and can lead to a spread of parasites.

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. However, this procedure requires anesthesia which makes it costly. At AnimalBiome we offer oral FMT capsules that make this process a little 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.

These two approaches combat harmful microbes:

6)    Antibiotics

This is the most popular and often necessary treatment. Antibiotics kill their targets by inhibiting essential life functions of the bacteria they are meant to kill. However, these essential functions are often shared by many more good bacteria than bad bacteria in the microbiome. Antibiotics deplete the microbiome and cause potentially permanent changes. If your dog needs to take antibiotics, you should also consider adding microbes (#1-5 above) to your dog’s microbiome 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. However, this is considered a last-resort response to fighting an infection.

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 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.

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.

I’d love to hear your comments or feedback. If you liked this article please consider sharing it.

Older Post Newer Post


Leave a comment

Please note, comments must be approved before they are published