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What lives in the dog’s and cat’s gut? Forgotten world of microbiome



Have you been wondering why the word microbiome has been increasingly popular topic in human and veterinary medicine? This is because scientists began to uncover that the microbes living on and in the body are not just a random cluster of germs originating from the environment that can make an individual sick. Nor are the gut microbes only important to herbivores to help them extract the energy from food. In fact, gut microbiota is a living ecosystem of commensal microorganisms that provides lots of benefits to every mammal from maintaining gut health to regulating distant organs. In return, the mammalian host (dog or cat) provides the microbiota with nutrients and stable environment. Research is clear that harboring a healthy microbiota in the gut offers many health benefits to dogs and cats. 

What is the size of gut microbiota of dogs and cats?

Gut microbiota is the entire habitat of living microorganisms, including not only anaerobic and aerobic bacteria but also archaea, fungi, protozoa, and viruses. They have been evolving for billions of years and there are thousands of diverse species known. It is estimated that the intestine of mammals contains approximately 1010 to 1014 microorganisms which is 10 times more than that number of cells within the body.1 Due to the small size of microbes and presence in high density, the microbial mass is not as large and heavy when compared to the rest of the body. The total bacterial counts increase along the gastrointestinal (GI) tract of dogs and cats, with numbers being lowest in the stomach and highest in the colon.

What benefits do dogs and cats get from the microbiota?

Traditionally, the gut microbiota are known to be a key player in digestion of foregut and hindgut fermenters like ruminants, horses, or rabbits, helping them to extract energy from otherwise indigestible feed by fermentation.  In fact, ruminants are totally dependent on microbial fermentation to survive. Although the energy derived from fiber fermentation in omnivores and strict carnivores is much less, dogs and cats have capacity to ferment undigested material in their colon for their benefit, including pathogen resistance, modulation of immune system, and synthesis of nutrients. Additionally, even in a true carnivore like the cat, microbes inhabiting the feline hindgut have been shown to be very active and have fermentative functions similar to those found in dogs, pigs, and humans.2  

Where do dogs and cats get their microbiota?

Puppies and kittens are born virtually without GI microbiota and their intestines are colonized by microorganisms from the birth canal and from the environment within 24 hours from birth. Those microbes are necessary to the newborn to establish an oral tolerance to commensal bacteria and food antigens, which ensure that gut immune system will ignore them and will not initiate an inflammatory response.  Throughout life, a balanced intestinal ecosystem continues to collaborate with the immune system and among multiple other roles, serves as the defense against invading intestinal pathogens.

Is the gut microbiota of dogs and cats unique?

While microbiota of individual dogs and cats have similar functions, recent studies conducted have shown that each dog and cat harbours a very unique and individual microbial profile.3,4 The main difference is in bacterial species and strains with minor overlap between individual animals. In one study, 84% of cats harboured Bifidobacterium species but only a minor percentage of cats harbored the same species of Bifidobacteria.4


In spite of existing differences in microbial species between individual dogs or cats, the metabolic end products formed do not markedly differ. This is because several members of microbial community are able to perform similar functions, and if one microbial group is displaced, other members of the community are capable of substituting that function and stabilizing the entire ecosystem.  As a result, there is a large similarity in the products of microbial fermentation among individual dogs and cats, in spite of, large differences of bacterial species involved in the process. Using an analogy, it doesn’t matter what kind of builders construct the house (or what bacteria do the work), as long as the house (or products of microbial metabolism) is built. 

Why does gut microbial ecosystem matter to dogs and cats?

Intestinal microbiota play an important role in the health of dogs and cats. Most of its action is located in the colon where the flow of ingesta slows down, which provides the ideal environment for the microbes to grow and multiply. Microbes are excreted with each defecation which means that this ecosystem is in a dynamic and constant state of turnover, growth, and replenishment. The balance of this ecosystem is established via various cooperative strategies that microbes developed and through this dynamic process, thus, the microbial community is capable of competitively excluding potentially pathogenic bacteria. 

Examples of functional contributions of the gut microbiota

Examples of functional contributions of the gut microbiota

What are some problems associated with an unhealthy gut microbiota?

Most of the commensal bacteria in the canine and feline gut are symbiotic; however, after translocation through the mucosa or under specific conditions, such as immunodeficiency, commensal bacteria could cause pathology.  A state when the bacterial populations within the GI tract become imbalanced is called dysbiosis.  Clinical disturbances of dysbiosis include indigestion, anorexia, diarrhea, and malabsorption of nutrients.17 Dysbiosis in dogs and cats has a number of causes and has been associated with both acute and chronic GI diseases18-21, antibiotic administration22, or can be diet-induced.23 In people, dysbiosis is also associated with atopy, obesity, liver disease, or GI malignancy. Conversely, normal gut microbial equilibrium is associated with health.


Evidence is accumulating to consider the gut microbiome as a central player in the gut‐kidney axis. Some microbial products, such as advanced glycation end products, phenols, and indoles, are uremic toxins which are absorbed into the circulation and cleared by normal‐functioning kidneys. In kidney disease, these products can accumulate and may contribute to the uremic load and increased morbidity.24


Bacteria in the gut also play a role in whether or not an individual becomes obese. This is linked to the ability of the intestinal biome to extract additional energy from undigested food and to regulate energy expenditure and storage.


Evidence increases that there is a gut microbe and the brain communication. Neuroscientists are probing the idea that intestinal microbiota might influence brain development and behavior, as well as anxiety. More research is needed to investigate this relationship in dogs and cats.

What is the best way to maintain gut microbial health in dogs and cats?

Microbial growth in the gut is influenced by multiple factors but the major determinant is the substrate for their nourishment, such as dietary fiber, residuals of undigested food, sloughed mucosal cells, or enzymes released into the gut lumen. Altogether, gut microbes use these substrates for their own benefit and growth. In return, they manufacture and release number of compounds called postbiotics, with many of them providing benefits to the host.25


Gut microbiome of dogs and cats can be modulated with diet composition, antibiotics, prebiotics, probiotics, or synbiotics. Prebiotics, probiotics, or synbiotics can be administered as dietary supplement or added to the commercially formulated pet food. Since they have to eat every day, choosing a complete and balanced food specifically designed to promote healthy microbial fermentation for dogs and cats is the most practical way to nourish healthy gut microbiota from day to day. Inclusion of prebiotic fibers into the food offers the most practical and lasting strategy to positively influence the intestinal microbiome. Not every prebiotic is created equal. Fibers with prebiotic benefits commonly found in pet foods include beet pulp, flaxseed, fruit fiber, rice fiber, fructooligosaccharides, inulin, oats, or barley.


Traditional viewing on gut microflora in veterinary medicine focused mainly on the role of microbes to ferment herbivorous diet and help herbivorous animals to extract energy from poorly digestible plant matter. However, research has shown that even omnivores and true carnivores like dogs and cats do benefit from balanced ecosystem in their gut. Gut microbiota is an important living ecosystem within the body, which influences both gut health and extra-intestinal organs. Gut microbes metabolize and ferment substances that travel to the hindgut in the form of undigested substrate. The composition of the intestinal microbiota ecosystem and postbiotics produced are strongly affected by dietary patterns. Composition of the diet and inclusion of prebiotic fiber represent a long-lasting strategy to consistently maintain balance of gut microflora and deliver health benefits.

Key Points

  • Microbiota of mammals contains trillions of bacterial cells, 10 times more cells than the number of cells constituting the body.
  • Gut microbiota influences many areas of dog and cat health from nutritional benefits, modulation of immune system, and protection of host against pathogens.
  • The benefits of microbiota to the host are mediated through postbiotics, or products of microbial metabolism with biological effects.
  • A dysbiotic state of the gut microbiota is associated with inadequate diet and in pathological conditions of gastrointestinal tract in dogs and cats.
  • Microbiota of dogs and cats should be considered a key aspect of animal health and nutrition.
  • Prebiotics in the diet produce lasting and positive impact on microbiota with a number of health benefits.
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Dr Iveta Becvarova, DVM, MS, DACVN Director, Global Academic & Professional Affairs, Hill’s Pet Nutrition Inc.


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