Feeding the Gut Microbiome

Health

Diet is the most powerful tool you have for supporting a healthy gut microbiome. Feeding your dog a minimally processed, meat-based diet can promote a more balanced and diverse gut microbiome compared to high-heat processed diets. The more diverse your dog’s gut microbiome, the better it is able to perform its functions and protect against harmful microorganisms.

Why Diet Matters For Your Dog’s Gut Health

Over 70% of your dog’s immune system is located in the gut, which shows how intimately connected nutrition is to your dog’s overall wellbeing. Research shows that high-protein, high-fiber, and low-carbohydrate diets create the optimal environment for beneficial gut bacteria in dogs. Using quality ingredients and a variety of nutrient sources further enhances these positive health effects.

What to Feed Your Dog’s Gut Microbiome

According to research from AnimalBiome, your dog’s gut microbiome may be able to be restored with these simple changes to her diet:

  1. Feed enough protein, such as beef, turkey, organ meat, eggs, etc.
  2. Provide adequate fiber, such as fiber-rich ingredients like broccoli and leafy green vegetables, or a powdered fiber supplement.
  3. Avoid high-carbohydrate diets, such as diets with refined carbohydrates like white rice.
  4. Add fermented foods, such as kefir and sauerkraut.

FEEDING ENOUGH PROTEIN

Protein essential building blocks that beneficial gut bacteria need to function properly:

  • When your dog digests protein, it creates compounds that help improve bacterial diversity throughout the digestive tract.
  • Adding more protein to your dog’s diet supports the growth of beneficial Fusobacteria. Low levels of Fusobacteria are associated with inflammatory bowel disease (IBD).

AVOIDING HIGH-CARBOHYDRATE DIETS

Dogs have zero requirements for carbohydrates, yet many commercial foods contain high levels of carbs. While carbs provide quick energy, too many can disrupt gut balance:

  • Excessive carbohydrates can lead to an overgrowth of harmful bacteria in the Firmicutes group, which in high numbers contribute to inflammation throughout the body.
  • In studies where dogs were fed high-protein, low-carb foods, the microbiomes of overweight dogs shifted significantly toward the balanced bacterial communities seen in healthy-weight dogs.

PROVIDING ADEQUATE FIBER

Fiber in the diet helps regulate bowel movements and keeps stool at an ideal consistency:

  • Feeding a diet higher in fiber has been shown to reduce gut inflammation in dogs with sensitive GI tracts. When bacteria break down fiber through fermentation, they produce molecules that are critical for combating inflammation.
  • Soluble fiber helps maintain blood glucose levels, while insoluble fiber helps form solid stools.

ADDING FERMENTED FOODS

Small amounts of fermented foods like kefir and sauerkraut are a great source of postbiotics:

  • Postbiotics ensure that cells get what they need to fulfill their functions and communicate effectively.
  • Research shows postbiotics can help improve symptoms in dogs prone to inflammatory conditions like itchy skin or digestive flare-ups.
  • While fermented foods can help maintain a healthy gut, they alone can’t provide enough microbial diversity to correct an existing imbalance.

PRACTICAL TIPS FOR FEEDING THE MICROBIOME

If your dog has been eating only one type of food for months or even years, slowly introducing more variety into her diet can strengthen her gut microbiome.

  • Consider transitioning your dog to high-protein, high-fiber, and low-carbohydrate diet.
  • If you can’t switch to a 100% minimally processed diet, add a variety of fresh food toppers to help promote a more diverse gut microbiome.
  • Add small amounts of fermented foods to your dog’s meals.
  • Use this calculator to calculate the carbohydrates in your dog’s food. Ensure your dog’s food contains at least 35% protein on a dry matter basis.
  • Be especially mindful of treats, which can be a significant hidden source of carbohydrates. Choose meat-based treats instead of carb-heavy commercial options.

Remember to work with your veterinarian when making any dietary changes to ensure it is safe and appropriate for your dog’s specific needs.

Any change to your dog’s diet or feeding schedule should be discussed with your veterinarian first to ensure it is safe and appropriate for your individual dog.

Dr. Katie Woodley, the founder of The Natural Pet Doctor, has been pioneering integrative veterinary medicine for the last 15 years. She blends Eastern and Western medicine to address the root causes of disease, with a focus on gut and skin health. Dr. Woodley creates comprehensive treatment plans combining targeted nutrition and herbal remedies to promote overall well-being in pups.

For more information, check out Dr. Katie Woodley’s Better Gut Health Blueprint.

For More Information:

  • 2025 The Natural Pet Doctor. Better Gut Health Blueprint.
  • Sandri, Misa et al. “Raw meat based diet influences faecal microbiome and end products of fermentation in healthy dogs.” BMC veterinary research vol. 13,1 65. 28 Feb. 2017, doi:10.1186/s12917-017-0981-z
  • Ganz, PhD, Holly. State of the Gut 2024. Oakland, CA, AnimalBiome, www.animalbiome.com/pages/state-of-the-gut-2024.
  • Dr. Katie Woodley – The Natural Pet Doctor. “Top Natural Ways to Help Your Cat and Dog Live Longer FREE Masterclass Replay.” YouTube, 21 June 2022, www.youtube.com/watch?v=sybGrXhHmvo. Accessed 20 Apr. 2025.
  • “Restore the Microbiome – AnimalBiome Veterinary.” Animalbiome.vet, 2015, animalbiome.vet/pages/restore-the-microbiome.
  • Schmidt, Milena et al. “The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets.” PloS one vol. 13,8 e0201279. 15 Aug. 2018, doi:10.1371/journal.pone.0201279
  • ‌Fritsch, Dale A et al. “Microbiome function underpins the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea.” BMC veterinary research vol. 18,1 245. 24 Jun. 2022, doi:10.1186/s12917-022-03315-3