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Restoring a Canine’s Intestinal Microbiome

James Odell, OMD, ND, L.Ac

Dogs like humans have a complex gut microbiome composed of bacteria and other microorganisms. This microbiome must stay ecologically balanced to keep the animal healthy and immunologically strong. Like humans, much of the dog’s gut microbiota is non-harmful (commensal) and play many important roles in a canine’s health (Eckburg, Bik et al. 2005). Commensal bacteria perform the following important functions:

  • Form a protective barrier against toxins, heavy metals and allergens

  • Produce enzymes for digestion

  • Produce B vitamins

  • Change the genetic expression of cells

  • Contribute up to 90% of the body’s immune system

  • Crowd out unwanted bacteria and fungi

  • Produce serotonin and impact mood

Germ-free animal studies have shown that an absence of microbiota is associated with poor immune system development and increased nutrient requirement (Gordon 1971). When dogs have an imbalance in their gut microbiome, they will exhibit several symptoms and abnormal behavior. Diarrhea, bad breath, gas and bloating are common signs of such an imbalance, as is eating grass or other animals’ poop. Grass contains many soil microorganisms and eating grass for a dog is an instinctual way to attempt to replace the intestinal microbiome with bacteria. Of course, this is not ideal, as much yard grass is often contaminated with lawn chemicals. Also, grass is not an abundant source of beneficial bacteria either. Other animals’ feces contain bacteria and enzymes as well; unfortunately, some contain very harmful or pathogenic bacteria and may further aggravate the dog’s microbiome. As humans we take probiotics and fermented foods to balance our gut ecology. This strategy can help dogs too. There are several pet probiotics on the market now, but it is important to understand which ones are best and why.

Comparatively little work has been done to characterize the canine gut microbiota compared to that of humans. Several culture-based studies have been conducted profiling the canine gut microbiota (Greetham, Giffard et al. 2002; Greetham 2003). Gut microbiota are composed of different bacteria species taxonomically classified by species, genus, family, order, class, and phylum. Each dog’s gut microbiota changes during their lifetime and its composition depends on many factors and exposures (types of food, exposure to antibiotics and drugs, vaccines, age, breed, social interaction and psycho-emotional health). Essentially, each dog’s intestinal microbiome is unique, just like a fingerprint, because every dog is exposed to a unique environmental terrain and diet.

Bacteria live in all parts of a dog’s digestive tract. There are just a few that live in the stomach and as you travel from the small intestine to the large intestine, the numbers increase. But, by far, most of the bacteria thrive in a dog’s colon. This microbial community is usually dominated numerically by strictly anaerobic species, typically including members of the bacteroidetes, bifidobacteria and clostridia (Savage 1977; Gill, Pop et al. 2006). Essentially, types of bacteria change as you move down the digestive tract. (see diagram)

Dogs like people have the same 6 bacteria phyla in their guts. The two phyla Firmicutes and Bacteroidetes represent 90% of a dog’s gut microbiota. Though there are only 6 phyla, each phyla contains an astounding number of different bacteria species and strains. In fact, it is estimated there are several thousand strains of bacteria in the intestines. This complex microbiome also includes yeasts, but is mainly bacteria. These bacteria all function together, and they work as an organ. In fact, some scientists call the microbiome “the forgotten organ” (Backhed, Ley et al. 2005; O'Hara and Shanahan 2006). Balish observed that isolated dogs had an increased observed bacterial diversity (Balish, Cleven et al. 1977). It was suggested that this may have been due to disruption of the dominant microbiota leading to an increase in previously repressed groups.

Here are some of the bacteria families found in the top three phyla:


  • Blautia

  • Clostridium

  • Lactobacillus

  • Bacillus Subtilis

  • Bacillus licheniformis

  • Pediococcus acidilactici

  • Enterococcus faecium


  • Bacteroides

  • Prevotella


  • Bifidobacterium





Much like humans, there are several species and strains of probiotics (primarily derived from the Firmicutes and Actinobacteria phyla) that are commercially available and can help restore a canine’s intestinal microbiome: Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus plantarum, Lactobacillus rhamnosus, Bifidobacterium longum, Enterococcus faecium, and the soil-based organisms - Bacillus Subtilis, Bacillus licheniformis, Bacillus coagulans, Bacillus indicus and Pediococcus acidilactici. All these organisms each have unique properties.

The soil-based probiotics are spore-forming. This means they can form a hard coating that protects them from heat, stomach acids and most antibiotics. The soil-based probiotics’ protective coating means they don’t need to be refrigerated. And unlike most probiotics that come from dairy (like Lactobacillus and Bifidobacterium), soil-based probiotics are hypoallergenic. That of course is better for dogs with food sensitivities and dairy allergies.

Probiotics can play an important part of a canine’s health plan (Biourge V 1998; Baillon, Marie-Louise A 2004; Kelly R 2010). They can help fight pathogenic bacteria and support the dog’s immune system (Pascher, M 2008). However, probiotic supplementation generally needs to be administered daily. In order to boost the numbers of diversity of bacteria in the dog’s microbiome it is also optimally better to periodically rotate species. 

Dog Food Considerations

Just like humans “dogs are what they eat”. What a canine’s diet is composed of hugely influences its overall health and their intestinal microbiome. To better understand what is best to feed a dog, it is useful to reference the history of commercial dog food. In 1918, WWI just ended and technology like cars and tractors eliminated the need for horses. This created a surplus of horses. A man named Phillip Chapel saw the opportunity to buy up cheap horse meat and sold the first canned dog food under the brand name Ken-L-Ration. Thus, Ken-L Ration became the first canned dog food in the United States. Though made of horse meat, it was carefully marketed as “lean, red meat” and only disclosed its ingredients in much smaller letters at the bottom of the packaging. By 1941, canned food was so successful that producers were breeding horses just for dog food and slaughtering 50,000 of them per year.

But when tin was rationed during World War II and pet food was classified as a “non-essential,” producers had to get creative. The combination of these imposed rations and pushback from animal lovers who were furious about the number of horses being killed every year for dog food, created a golden opportunity to introduce a new product in the pet food industry.

General Mills acquired Spratt’s in 1950, and Purina entered the dog food market in 1956 with the first ‘kibble’. Purina previously had been selling food for farm animals that was plant and grain-based for pigs and chickens. The Ralston Purina Company began experimenting with the machines they were using for their Chex breakfast cereal to create a more palatable dog food. Given the rations on tin cans, cardboard cereal boxes seemed like the perfect alternative for storing shelf-stable pet food. In 1956, the first dry kibble was produced through a process called extrusion

Extrusion is a method used for manufacturing large quantities of shelf-stable foods. It works like this: wet and dry ingredients are mixed to form a dough-like consistency, which is then fed into a machine called an expander. The dough is cooked under extreme pressurized steam and high temperatures before being extruded (or pushed) through a die cut machine and forming the small shapes we recognize as kibble today. This process, of course, destroys enzymes and many heat sensitive nutrients necessary for digestion and health. The extreme heat and drying remove beneficial vitamins, nutrients, and moisture that pets need to truly thrive. Different types of acrylamide and other carcinogens are also created in this process that could be detrimental to a canine’s long-term health. Kibble is a low-moisture product, which puts a dog in a constant state of dehydration. This created many diseases in dogs as pet food not only lacked enzymes and certain nutrients, but was composed of meat by-products and numerous toxic chemicals. Even worse is that these pet feeds were then allowed to contain diseased animal material and meat ingredients sourced from non-slaughtered animals - with no disclosure requirement. Of course, a dog’s intestinal microbiome suffers from such denatured, dehydrated food, as there is also a risk for bacteria and mycotoxins to be present. 

The use of extrusion for commercial kibble production gained momentum throughout the 1960s and 1970s as companies used the technology to create new flavors and varieties. Once kibble had been established as the leading pet food option, advertising strategies became more niche-based to differentiate brands. By the 1980s, Hill’s Pet Nutrition had introduced prescription kibble for different ailments (like kidney and liver failure) and continued to diversify by the 1990s, producing kibble based on individual activity level for weight management.

Today, pet food companies still produce kibble by extrusion because it facilitates flexibility and density control and better pasteurization. All ingredients (yes, even the high quality or organic variety) are cooked at the same extremely high temperatures and then dried after extrusion in order to remove moisture. While this process optimizes product shelf-life, it can also significantly impact the nutrient composition of the food and poses many other health risks. Additionally, much of the commercial pet food landscape has become increasingly unregulated and is marked by frequent recalls and health controversies.

Dogs are considered opportunistic carnivores, meaning they are primarily meat eaters but can supplement with food from other sources. Bottom line is individual dogs have different needs and should be fed as individuals, not a “one size fits all” diet. This means that different dogs may be better off eating different diets. However, there are some generalities that can be observed. The optimal diet for dogs includes fresh, whole foods made from human-grade ingredients. They should be grass-fed, free-range and organic, if possible. The optimal diet includes healthy fats, high moisture (around 70%) and is a healthy balance of protein, carbohydrates and other nutrients. One way to feed this balanced diet is with raw food. A raw diet for dogs includes simply fresh, whole foods that are uncooked and minimally processed. Meats and greens that are fresh, uncooked and wild make up the diet that dogs evolved to eat. It is what canine species in the wild still eat. The administration of a raw food diet has been shown to promote a more balanced growth of bacterial communities and a positive change of healthy gut functions in comparison to a commercial extruded diet of kibbles (Sandri, M 2016; Kim J 2017; Schmidt, M 2018; ).

Raw food is more easily absorbed and contains vital naturally occurring enzymes and vitamins that cooking destroys. Living foods that are unprocessed, fresh and whole enable our pets to thrive. And it’s the diet that lets dogs be their happiest and healthiest. Going raw does not have to be an all or nothing approach. Frozen raw dog food provides a complete and balanced, diversified diet. Most of these products can be obtained at health food stores or animal supply stores and contain 100% grass-fed beef, free-range poultry, and other non-factory farmed animal protein sources. Adding even small amounts of raw to a dog’s diet has shown to improve their overall health (Reinerth, S 2014; Stogdale, L 2003; Herstad K 2017).

When switching from dry food, it is common to see significant weight loss in the first week which is primarily water weight. After this, it is important that they lose no more than 1 – 2% of their body weight per week. It is highly recommended to consult and work with a holistic veterinarian to assist in monitoring your dog during any dietary transition.

Importance of Fiber

Every time a dog eats, the nutrients are not just feeding his cells, it is also feeding the intestinal bacteria. Thus, bacteria eat exactly much of what dogs eat. The commensal (friendly) bacteria love one food in particular: fiber. That is because dogs generally cannot digest fiber, so it passes undigested to the colon, creating short chain fatty acids (SCFAs) and benefiting the colonic bacteria (Gibson, 1995; Panasevich, M 2015). When bacteria eat fiber, they generate byproducts called short chain fatty acids. SCFAs either remain in the dog’s colon or they are excreted from their body. Either way, they play a critical role in a dog’s health and immunity:

  • SCFAs (especially butyrate) build important T-cells in the immune system, which helps reduce chronic inflammation.

  • SCFAs feed and grow more commensal bacteria and discourage the growth of harmful bacteria.

  • SCFAs help form the protective mucus layer in the gut. 

  • SCFAs keep the cells lining healthy preventing altered bowel permeability.

  • SCFAs reduce glucose levels, which protects against metabolic disease and obesity.

  • SCFAs protect against food allergens.

  • SCFAs help the body absorb calcium, magnesium, iron and other nutrients.


Like humans, gastrointestinal microbiome dysbiosis is common in dogs and can jeopardize their health leading to degenerative diseases and early death. The gut microbiota of dogs is significantly influenced by diet type (i.e., natural diet (raw) and commercial feed). Specifically, dogs fed a natural diet have more diverse and abundant microbial composition in the gut microbiota than dogs fed a commercial feed. Overall, some degree of a high-quality raw food diet containing nutrient rich fiber together with probiotic supplementation can yield tremendously beneficial effects on microbial populations and the systemic immune characteristics of a dog. 


The information in this article is not intended to replace the advice of your own veterinarian or doctor. This BRMI e-journal article is designed for information purposes only - so that you will know what options might be available to you and what questions and topics to ask your own veterinarian about. Only vets who have directly examined your pet can tell you which diet and supplements are most effective and safe for your animal. Recommendations as to diet, supplemental therapeutics and best standards of practice are constantly evolving in the veterinary industry and, at any one time and on any one point, opinions between professionals may differ. Please do not use this e-journal article as a sole source of information on any matter of veterinary or human health interest.


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