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Healing Your Dog’s Gut Protocol

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The 4 R Protocol offers a step-by-step framework to healing your dog’s gut by addressing root causes rather than only managing symptoms.

THE 4 R PROTOCOL TO HEALING YOUR DOG’S GUT

By systematically removing triggers, replacing them with healthy alternatives, repopulating the gut with beneficial bacteria, and repairing the damaged gut lining, the 4 R Protocol provides a comprehensive solution to gut health issues:

  1. Remove harmful elements that damage gut health.
  2. Replace with healing nutrition and digestive support.
  3. Reinoculate with beneficial bacteria to restore healthy gut flora.
  4. Repair the gut lining with targeted nutrients.

Always work with a veterinarian knowledgeable in this protocol to tailor this approach to your specific dog’s needs.

1. REMOVE

Eliminate all potential triggers by identifying problem foods:

Elimination Diet:

  • Remove all proteins, carbohydrates, and fats your dog has consumed in the past six months.
  • Continue for 2-3 months (timing varies based on symptom severity).

Food Sensitivity Testing:

  • Identify specific foods that may be causing an adverse reaction.
  • Best if used as a general roadmap, rather than a definitive result as false-positive and false-negative results are common.

Foods to Eliminate:

  • Common food sensitivities in dogs are chicken, beef, dairy, and wheat. True food allergies only affect about 3.5% of dogs.
  • Histamine-releasing foods, such as fermented foods like sauerkraut, yogurt, and canned fish, can trigger inflammation in your dog’s body.

3. REINOCULATE

Introduce beneficial bacteria to support gut health.

Probiotics: Beneficial organisms that strengthen the gut’s microbial community and create conditions where existing healthy bacteria can flourish.

Fecal Microbiota Transplant (FMT):

  • A treatment that transfers stool from healthy dog donors to restore gut balance in dogs with digestive issues.
  • FMT capsules introduce a diverse community of beneficial bacteria and replenish your dog’s microbiome with the right bacteria in the right proportions.

2. REPLACE

Introduce healthier alternatives and establish a strategic eating pattern.

Developing a Rotation Diet:

  • Work with a professional to create three distinct diets with different protein, carbohydrate, and fat sources to feed in rotation.
  • Ensure all diets exclude identified allergens/sensitivities.
  • Continue diet rotation for 3-6 weeks (up to 12 weeks in severe cases).

Diet Recommendations:

  • Nutritionally complete homemade meals are preferred for complete ingredient control.
  • Cook foods slowly at low temperatures to prevent advanced glycation end products (AGEs) created by high-temperature cooking methods.
  • Limit treats to ingredients included in the day’s rotation diet.

Monitoring Progress:

  • Keep a detailed food journal to track reactions. Sensitivities may take up to 3 days to appear.

4. REPAIR

Support gut healing by gradually introducing supplements.

Key Supplements:

  • Saccharomyces boulardii: Controls diarrhea, stimulates secretory IgA production to help immune system, regulates microbiome and gut motility  (the movement of food through the gastrointestinal tract).
  • Omega-3 fatty acids: Reduces inflammation and regulates microbiome.
  • L-glutamine and zinc carnosine: Support gut healing.
  • Herbal combinations: Slippery elm powder, marshmallow root powder, and licorice root.

MAINTAINING GUT HEALTH

Your dog’s ability to heal depends significantly on her overall stress burden. Environmental factors like noise levels, overcrowding, and unpredictable schedules can all contribute to your dog’s stress load and potentially slow gut healing. To create an environment conducive to healing, focus on these key lifestyle factors for your dog:

  • Manage your own stress (your stress levels directly impact your dog’s stress).
  • Provide daily exercise, especially outdoors.
  • Create environmental enrichment opportunities.
  • Maintain consistent routines.

Healing your dog’s gut is a journey that takes time, but each small step creates meaningful progress.

Always work with a veterinarian knowledgeable in the 4 R Protocol to tailor this approach to your specific dog’s needs. Any change to your dog’s diet or feeding schedule should be discussed with your veterinarian first.

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.
  • ‌Silver, DVM, Rob. “An Integrative Approach to Maintaining a Healthy Gut.” DVM 360, 5 Jan. 2022, www.dvm360.com/view/an-integrative-approach-to-maintaining-a-healthy-gut.
  • Ganz, PhD, Holly. State of the Gut 2024. Oakland, CA, AnimalBiome, www.animalbiome.com/pages/state-of-the-gut-2024.
  • Roberts, DVM, Ruth. “A Nutritional Approach to Leaky Gut Syndrome in Dogs & Cats | IVC Journal.” IVC Journal, 2 May 2024, ivcjournal.com/a-nutritional-approach-to-leaky-gut-syndrome-in-dogs-and-cats/.
  • ‌“Fecal Microbiota Transplant – AnimalBiome Veterinary.” Animalbiome.vet, 2015, animalbiome.vet/pages/fecal-microbiota-transplant?srsltid=AfmBOor3qqt5kKqixmaQliWQJr8zffx6j_3ZQT3eYtl46p-Di9n3wZfE.

Disclosure: This post contains affiliate links. If you make a purchase through these links, The Doggy Dish™ may earn a small commission at no extra cost to you. We only recommend products we personally use and trust.

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