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