Your Dog’s Healthy Gut

Here’s how to make an affordable investment in dog gut health.


DNA research has documented the importance of gut microbes in human and canine health, immunity, and longevity. A healthy microbiome—an umbrella term used to describe communities of bacteria, fungi, and other microbes in the body—destroys harmful pathogens, including disease-causing viruses, fungi, bacteria, and parasites. Most reside in the intestines, where they are known as the “gut microbiome.”

In a healthy gut, “friendly” or beneficial microbes secrete chemicals that destroy harmful bacteria and, if they are present in sufficient numbers, colonies of beneficial bacteria starve harmful microbes by depriving them of nutrients and space. In addition, the microbes in a healthy microbiome can bind to toxins, such as allergens and substances that cause cancer, removing them from the body through normal elimination.

Your Dog’s Microbiome

At 6 months of age, the gut microbiomes of healthy puppies contain over 500 different types of microbes. Though the numbers decline as dogs age, older dogs still have over 400 different types of bacteria and other microbes in their digestive tracts, approximately 80% of which are beneficial and 20% potentially harmful.

An estimated 70-80% of your dog’s immune system is in the microbiome. Dysbiosis (an imbalance of healthy or beneficial microbes in a dog’s body) leads to a variety of common symptoms that can be treated by improving a dog’s gut health, including:

  • Allergies, itching, and food sensitivities
  • Indigestion, diarrhea, constipation, and flatulence
  • Skin and coat problems
  • Dental problems and gum disease
  • Bad breath and unpleasant body odors
  • Arthritis or joint pain
  • Liver disease
  • Pancreatitis
  • Respiratory problems
  • Inflammation
  • Obesity
  • Diabetes
  • Susceptibility to infections

What Causes Gut Imbalances?

The simplest answer to what most affects dog gut health is modern life. Most American dogs eat processed foods and even the highest-quality kibbles are high in carbohydrates and low in enzymes and nutrients that are damaged by the heat and pressure of manufacturing. Add environmental factors like harmful chemicals, EMF (electromagnetic frequency) exposure, air or water pollution, and other 21st century stressors, and it’s no wonder our dogs are affected.

A Gut-healthy Diet

Holistic veterinarians have long argued that the most important factor in a dog’s health is food. A species-appropriate diet (also known as a biologically appropriate diet) is modeled after what wild canines consume, which is mostly the raw meat, bones, glands, blood, skin, and organs of prey animals. The natural canine diet is high in protein, moderate in fat, and low in carbohydrates.

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According to Karen Becker, DVM, whose popular books include Dr. Becker’s Real Food for Healthy Dogs and Cats (Natural Pet Productions, 2018) and The Forever Dog: Surprising New Science to Help Your Canine Companion Live Younger, Healthier, and Longer (Harper, 2021), dogs fed fresh in place of dry dog food show positive microbiome changes and improved overall gut function. “A nutritionally optimal, species-specific, fresh raw or gently cooked diet is always a better choice for pets than extruded kibble diets,” she says.

Frozen fresh, lightly cooked, and freeze-dried raw diets represent the fastest growing segment of today’s pet food industry. Look for frozen raw SmallBatch, A Pup Above, Stella & Chewy’s, Primal, Northwest Naturals, and similar dog foods in independent pet supply stores. You can feed your dog from scratch with the help of books like Dr. Becker’s, but brands like these are an easy way to provide the complete nutrition and variety that build a better microbiome.

Gut Health Supplements

In addition to feeding an appropriate diet, you can enrich your dog’s microbiome by adding prebiotics and probiotics to her food.

  • Prebiotics are indigestible carbohydrates, such as fiber, that feed and support the beneficial bacteria that live in your dog’s digestive tract.
  • Probiotics are live microbes that regulate immune response, produce short-chain fatty acids that have anti-inflammatory properties, prevent the overgrowth of harmful microbes, and help prevent leaky gut syndrome by strengthening the gut barrier.

Both are familiar supplements for pets as well as people, and several brands combine active bacteria with the fibrous foods that feed them. A leading theory about the effectiveness of probiotics is that the more different strains of beneficial bacteria they contain, or the more species-specific they are (derived from cat, dog, or wolf sources), the more likely they are to improve your animal’s microbiome. Most probiotic activity occurs in the intestines, which is why recommended brands use strains of beneficial bacteria that survive stomach acid.

Research shows that the popular probiotic strain Bifidobacterium animalis helped reduce stress in dogs moved to kennels from their homes and that it was as effective as antibiotics in treating severe diarrhea. The beneficial bacterium Bifidobacterium longum reduced overall anxiety in 90% of the dogs tested with it, and B. longum and other probiotics have been shown to reduce digestive problems. Probiotics are often prescribed for dogs recovering from antibiotic therapy, which kills both harmful and beneficial bacteria.

The strength or concentration of probiotic products is measured in CFUs, or Colony Forming Units. Most probiotics sold for human or pet use contain at least 1 million CFUs per serving, but many measure their CFUs in the billions. Check labels to compare brands.

For example, Purina’s  FortiFlora Canine Probiotics Supplement  is sold for the dietary management of diarrhea and to help prevent flatulence. Available as a powder to sprinkle over food or as chewable tablets, the recommended dose of FortiFlora contains 100 million CFUs of a single beneficial bacterium, Entercoccus faecium. In contrast, Bark & Wiskers Complete Probiotics for Pets contains 15 strains of probiotics totaling 38 billion CFUs, Nulo Gut Health Functional Powder For Dogs and Nulo Probiotic Soft Chew Supplements for Dogs  contain 5 strains of probiotics totaling 1 billion CFUs, Adored Beast Roots contains 3 species-appropriate ancestral probiotic strains from wolves totaling 15 billion CFUs, Adored Beast Love Bugs contains 14 strains of probiotics for dogs and cats totaling 30 billion CFUs, and Primal Frozen Raw Fermented Goat Milk contains 3 strains of probiotics totaling 5 billion CFUs per fluid ounce (2 tablespoons).

In addition, you can help improve your dog’s microbiome by following these simple tips:

  • Keep your dog hydrated by encouraging him to drink, making clean water available indoors and out, and by adding fluids like goat milk, bone broth, or warm water to food.
  • Add fermented foods such as plain (unflavored, unsweetened) yogurt, kefir, cottage cheese, or raw fermented milk from cows or goats. For how-to instructions see “Dogs and Dairy Products.”
  • Examine dog food ingredients to be sure they are the best you can afford, focusing on good protein sources.
  • Rotate from one protein to another, a strategy that provides more complete nutrition than feeding the same food at every meal.
  • Limit or avoid carbohydrates, especially corn, wheat, and soy, which are commonly associated with allergies and digestive problems and which canines in the wild never consume.
  • Add fresh, whole raw, or gently cooked ingredients from your own dinner preparation whenever it’s convenient.
  • Add small amounts of dandelion greens, brussels sprouts, okra, asparagus, avocado (without the pit or skin), or nori/seaweed as meal toppers or mix them into your dog’s food.

Replacing as little as 20% of your dog’s dry or canned dog food with fresh ingredients can significantly improve gut health.

For more see  “What Do Probiotics Do for Dogs” in the August 2022 Whole Dog Journal and  ”A Better Biome.”