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Dog Gut Health Explained


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Many different factors affect dog gut health, including diet, nutrition, genetics, and infectious diseases. All of these factors play a role in regulating the bacteria that live inside your dog’s gastrointestinal (GI) tract, which in turn affect their digestive health.

Knowing how to maintain your dog’s gut health and what signs to watch for can help you prevent or resolve digestive distress, like diarrhea, when it occurs.

How the microbiome affects dog gut health

Your dog has a unique collection of hundreds of different types of bacteria and other microbes (such as viruses and fungi) in their GI tract, referred to collectively as the gut microbiome

Research has shown that the microbiome has a significant impact on gut health. These microbes help your dog digest food, support their immune system, and perform other important functions. The gut microbiome communicates with other areas of the body, including the skin and brain. 

Certain diseases, changes in diet, medications, and genetic predispositions can disrupt the balance of “good” and “bad” bacteria, affecting your dog’s gut health. Potential signs of an unbalanced gut microbiome include diarrhea, constipation, vomiting, and weight changes. These conditions can become chronic, requiring changes to nutrition or supplementation to better support the good bacteria. 

How diet affects dog gut health

Diet and nutrition changes are directly related to a dog’s gut health. The gut microbiome responds to changes in both the macro- and micronutrients that a dog eats. Changes to the amount of protein or fiber in a dog’s diet can shift the bacterial population in predictable ways (Pilla, 2021). Those changes can be reversed if the dog doesn’t maintain the same diet in the long term. 

A common example that veterinarians often see in the clinic is when a dog eats table scraps that they are not used to, causing acute onset vomiting and diarrhea. The sudden change in diet causes a short-term imbalance of the gut microbiome. It can be easily corrected simply by restoring a dog’s regular diet. 

While table scraps are an example of short-term diet changes, poor diets or food allergies can cause more chronic gut health issues in dogs. These types of long-term nutrition concerns can result in obesity, low body weight, itchy skin, and intermittent diarrhea.

How to test your dog’s gut health

Testing your dog’s gut can reveal whether their gut microbiome is in a healthy state or could use extra support. For a detailed breakdown of your dog’s gut health, try the Gut Health Test (powered by AnimalBiome). This at-home test detects bacterial imbalances and provides actionable insights for personalized diet, supplement, or lifestyle changes to improve your dog’s gut health.

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Learn more about our partnership with AnimalBiome and how we’re working together to improve canine health.

Signs of poor gut health in dogs

Some signs of digestive distress may be obvious, such as diarrhea. The following signs may indicate other gut health issues:

  • Excessive drooling
  • Vomiting or regurgitation
  • Diarrhea
  • Constipation
  • Loss of appetite
  • Fatigue or lethargy
  • Abdominal pain or bloating
  • Sudden weight gain or loss
  • Dehydration

If your dog starts showing any of these signs, talk to your veterinarian.

Learn more about what to do if your dog has diarrhea and special considerations for treating diarrhea in puppies.

Breed-specific diseases affecting gut health

Breed also plays a role in dog gut health. Multiple breeds are predisposed to specific diseases affecting gut health: 

  • Granulomatous colitis is associated with invasive E. coli in Boxers and French Bulldogs (Dogan, 2020). 
  • Miniature Schnauzers are predisposed to pancreatitis and often have hypertriglyceridemia (Xenoulis, 2010). 
  • Small and toy breeds are more likely to develop acute hemorrhagic diarrhea syndrome (also known as hemorrhagic gastroenteritis), a disease that is only recently becoming better understood. Affected dogs often have high numbers of the bacterial species Clostridium perfringens, a common cause of food poisoning, in the duodenum of their small intestines (Gaschen, 2018). 
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Knowing the breeds in your dog’s genetic ancestry can help identify gut health issues and other genetic health risks that they may be predisposed to. For example, at Embark, we test for genetic variants associated with cobalamin malabsorption. This is a gastrointestinal disease that prevents dogs from absorbing cobalamin, also known as Vitamin B-12. Dogs who have this disorder grow very slowly and have low energy levels. The good news is that this condition can be managed if it’s diagnosed and treated at an early stage.

Gut health supplements for dogs

Certain supplements can help support the gut microbiome. These supplements promote growth of good bacteria and provide nutrients for healthy digestion and solid stools.

Not all gut health supplements are equal. It’s important to know which supplements contain ingredients backed by research, as well as any side effects that may occur. Learn more about probiotics, prebiotics, and other gut health supplements for dogs.

How to improve dog gut health

There are several ways to help your dog maintain or improve their gut health. A balanced, nutritious diet is a great place to start. 

Other ways you can improve your dog’s gut health include:

  • Increasing the amount of fiber in their diet 
  • Minimizing table scraps and “junk food” meant for humans, such as sugary treats or dairy products 
  • Making sure they get regular exercise
  • Providing supplements, including probiotics, if they need digestive support
  • Maintaining a proper weight and body condition score

Feeding your dog a healthy diet and taking them to the clinic for routine veterinary checkups can help them stay in good health for years to come.

Kari Cueva, DVM

Dr. Kari Cueva, DVM, is the Associate Director of Veterinary Genetics at Embark. She is a 2011 graduate of the University of California, Davis College of Veterinary Medicine. Her research background includes four years in canine genetics with Dr. Mark Neff, and genetics fellowships at Cornell University and the National Institutes of Health. She continues to practice emergency medicine at a local animal hospital.

Read more about Kari Cueva, DVM

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