Your Dog’s Microbiome – What You Should Know

The dog’s gut microbiome and its impact on health and disease are of great interest to nutrition researchers. However, many dog owners are not quite sure what this term refers to, what the microbiome actually does, and how the food that they feed to their dog may influence their dogs microbiome and health. So, what is most important for you to know?

What is the Gut Microbiome?

The gut microbiome, more correctly referred to as the intestinal microbiome, is comprised of all of the microorganisms (primarily bacteria) the live within a dog’s intestinal tract. When counting from the mouth to the end of the large intestine, there are literally trillions of cells involved. By any measure, this is a whole lot of bugs.

The relationship between these organisms and the host animal (in this case, the dog) is truly symbiotic (mutually beneficial). A healthy dog and his bugs coexist nicely, with both deriving benefits from their living arrangement. The dog provides a warm place to live, plenty of food, and the company of other bugs. In return, the gut microbes have numerous functions that benefit the dog. They break down (ferment) certain food components and produce a set of beneficial nutrients and other end products, called postbiotics. These compounds nourish cells lining the intestine and, when absorbed, influence the dog’s nutritional status, health, and possibly even behavior.

A few specific examples:

  • Immune System: Bacterial populations function to “educate” the dog’s immune system regarding discrimination between innate, harmless bacteria and potentially pathogenic microbes, viruses and even diet components. (Yes, this over-simplifies it).
  • SCFAs: Certain species produce short-chain fatty acids (SCFAs) as end products. These compounds modulate the pH of the intestinal environment, have a role in satiety (feeling full after a meal) and provide an important energy source to cells lining the dog’s intestine, among other benefits.
  • Serotonin: More than 80 percent of the body’s serotonin, an important neurotransmitter, is produced from the amino acid tryptophan by intestinal microbes (yeah, wow!). This discovery was the impetus for the relatively new theory of the gut-brain axis and its effects upon behavior, which is a booming field of scientific inquiry.
  • Vitamin K: Intestinal microbes provide most (if not all) of a dog’s Vitamin K requirement. Although there is not consensus, there is some evidence that healthy dogs do not have a dietary requirement for this vitamin, as their needs can be completely provided by their gut microbes.

What Bugs?

The concentrations of microbes and the prevailing bacterial species differ significantly depending on the part of the intestinal tract that you are looking at. For example, a completely different set of bugs inhabit a dog’s mouth compared with what you find in the same dog’s large intestine. Generally speaking, the bugs that we are most interested in and that are most important in terms of the benefits that they provide, are those located in the large intestine. Most of these bacterial species come from five taxonomic phyla that are common to the microbiome of all dogs. Three of these, Fusobacterium, Bacteroides and Firmicutes, make up the largest proportion of fecal microbes. It is important to note that a phylum is a pretty darn large group of bugs. For example, Firmicutes, the largest phylum of bacteria, includes over 200 different genera and species that number in the thousands. That is a lot of bacterial diversity, no doubt!

Lactobacillus acidophilus – One species within the Firmicutes phylum

When dogs become ill, especially in the case of chronic gastrointestinal disorders, extreme changes can occur in both the species and the numbers of microbes that make up the gut microbiome. For our purposes in this essay, we will examine the gut microbiome of healthy dogs and take a look at what we currently understand about how what we feed dogs influences the make-up of their gut microbiome.

Feeding the Gut (Microbiome)

I have written extensively about the importance of feeding our dogs foods that are highly digestible. Foods that are well digested are broken down largely in the small intestine. The resulting nutrients are absorbed and provide essential functions in the body. Any undigested or partially digested food travels on to the large intestine where it provides food for gut microbes. The composition of these undigested food stuffs – protein, fat, carbs, fiber – play a significant role in determining the types of bugs that proliferate and dominate in an individual dog’s large intestine. Ultimately, the numbers of these bugs and the end products that they produce influence the dog’s health and wellness.

So, what dietary factors are important to consider?

Protein vs. Carbs/Fiber

Simply changing the proportion of protein or carbohydrate in a dog’s diet can lead to rapid changes in the composition of intestinal microbiota. Increases in plant carbohydrates and fiber lead to an increase in Firmicutes genera, several of which are “fiber fermenters,” associated with the fermentation of dietary fiber and the production of short-chain fatty acids. One of these SCFAs is a compound called butyrate, which is an important source of energy for cells lining the dog’s intestine. The use of prebiotics is an approach to increasing these microbes and their production of beneficial SCFAs (see below).

Conversely, when dogs are fed a high protein, low carbohydrate food, Firmicutes bugs decrease in number while other bacterial species increase. The increases are usually in the Proteobacteria and Fusobacteria genera, and include species that are important for the fermentation of protein (see “Protein – Are We Feeding Too Much?”). Interestingly, it appears that the source of the protein in a high protein food is less important than is protein level. Gut microbiome compositions were similar when dogs were fed a high protein food composed primarily of plant-based protein sources with when they were fed a food containing the same level of protein supplied by a mix of animal- and plant-source protein sources.

Cooked vs. Raw

Several studies have examined changes to dogs’ microbiome when switched from an extruded dry (kibble) food to a raw meat diet. In all cases, feeding dogs a raw food was associated with modified bacterial populations and in some cases, with an increase in both total numbers and microbial diversity when compared with dogs fed extruded foods (see “A Few Raw Facts“). However, because the raw diets were consistently higher in protein and fat and lower in carbohydrate, it is not known if the changes that were observed were due principally to macronutrient differences (higher protein), processing differences (raw), or a combination of these factors. The duration of feeding must also be considered, as most studies involved only several weeks of feeding. However, one report followed a group of 6 dogs that were fed a raw diet for 12 months. The dogs developed a more rich (i.e. diverse) and stable gut microbiome when compared with dogs fed a kibble diet during the same period. Finally, it is important to note that an increase in microbial number is not necessarily a benefit. Dogs fed raw foods may have higher levels of pathogenic microbes in their feces and may be at increased risk of infection (see “The Raw Deal“) .

Protein Quality

This is an important one. Protein quality is determined by a protein source’s amino acid composition and it’s digestibility. Feeding a high quality protein source at optimal levels results in minimal amounts of undigested protein entering the large intestine. Conversely, when dogs are fed poor quality protein, a relatively larger proportion of undigested protein enters the large intestine. Bugs there are happy to see this protein and rapidly digest it – a process aptly called putrefaction. Some of the end products of microbial putrefaction are considered to be harmful to dogs’ health. These are implicated in a number of chronic inflammatory disorders such as atopy (topical allergies), renal disease, and several forms of gastrointestinal disease. To minimize these effects, an important dietary goal is to provide an optimal level of high quality protein in dogs’ diets.

Clostridiaceae – Good or Bad?

Recent research suggests that the protein story may actually be a bit more complicated.

Because of a family of bacteria called Clostridiaceae.

One microbiome change that is consistently observed with both high protein and raw diets is an increase in Clostridiaceae species. We typically think of these organisms as pathogens, both for humans and for dogs – consider Clostridium perfringens and Clostridium difficiles. However, as an entire family of bugs, Clostridiaceae includes many genera and species. The taxonomic diagram below shows that Clostridium is only one of 15 genera within this family.

It has been suggested in recent years that the increase in total Clostridiaceae that is observed when dogs are fed high protein (and/or raw) foods, in contrast to earlier beliefs, may not be detrimental to dogs’ health and may come with certain benefits. An increase in this family of microbes has been associated with improved protein digestion and also with the production of butyrate. Remember, butyrate is the SCFA that provides energy to gastrointestinal tract cells – an increase that is considered to be beneficial. An increase in these bugs has also been positively correlated with improvements in fecal scores (i.e. firmer poops). Finally, one particular species, Clostridium hiranosis is associated with efficient bile acid metabolism and is reported to decrease in dogs with gastrointestinal disease. The bottom line is that an increase in Clostridiaceae species in dogs may not unequivocally be associated with negative health effects, as it is in other species such as humans. The jury is still out on this one. Stay tuned.

Prebiotics and Probiotics

Finally, how might the inclusion of prebiotic and probiotics in our dogs’ diets help to support health or prevent disease?

Prebiotics: The term prebiotic refers to selectively fermented ingredients that provide food for beneficial intestinal bacteria while not feeding the less desirable bacterial species (in some cases, potential pathogens). Prebiotics are either incorporated directly into a food or provided as a nutritional supplement (sometimes in combination with a probiotic).

Most prebiotics are types of fiber or resistant starches that are moderately to highly fermentable by gut microbes. Examples are fructooligosaccharides (FOS), beet pulp, potato fiber, and inulin, among others. Because they are indigestible (i.e. cannot be broken down by the dog’s digestive enzymes), prebiotics bypass the small intestine and end up in the large intestine, where they are fermented to varying degrees by gut microbes. The expected health benefits to the dog arise from two things:

  1. End products of fermentation: The bugs ferment the prebiotic as a source of energy and subsequently produce SCFAs. These compounds provide energy for the dog’s intestinal cells, reduce the pH of the intestinal environment, and induce a number of anti-inflammatory changes in the gut (and possibly in the body as well). There is also some evidence that prebiotics can protect the cells lining the gut by increasing the thickness of the mucus layer, affecting microvilli growth, and preventing adherence of pathogenic bacterial species. (These are all good things for the dog).
  2. Promotion of “good bugs”: Though research results are not consistent, there is some evidence that feeding prebiotics can increase the numbers of desirable fecal bacteria such as Bifidobacteria and Lactobacillus in healthy dogs.

However……results of studies with prebiotics in dogs have shown that beneficial alterations to gut microbe populations are influenced not only by the mixture of fibers that are fed, but also by the diet’s underlying carbohydrate and protein levels and by the host animal’s baseline microbial populations. Additionally, a rather thin line exists between feeding levels of prebiotic fibers that provide benefit versus a higher level that leads to loose stools and diarrhea (oops). So, once again, its complicated.


Probiotics: While prebiotics are compounds intended to feed a dog’s microbiome, probiotics are the bugs themselves. These are (usually) formulations of live organisms delivered in amounts that are intended to alter the microbiome in beneficial ways. The two most commonly used bugs are the two mentioned above – species of Bifidobacteria and Lactobacillus, although others have also been studied. Most of the studies of probiotic use with dogs have targeted dogs with gastrointestinal diseases such as acute gastroenteritis (i.e. garbage gut or stress diarrhea) or more serious disorders such as inflammatory bowel disease or protein-losing enteropathy. While there is some research suggesting possible benefits to ill dogs, there are no data to date that suggest health benefits of probiotics when provided to healthy dogs.

Take Away for Dog Folks: Here are the cliff notes:

  • The relationship between dogs and their gut microbiome is mutually beneficial. A healthy dog provides a great environment for a wide variety of microorganisms. The bugs, in turn, produce a variety of postbiotics and support health and wellness. A win-win for both.
  • Dietary factors that significantly influence the make-up of a dog’s gut microbiome include the amount and type of starch and fiber, the level and quality of protein, and whether the food is cooked (extruded) versus raw. A special call out to protein quality – pay attention to it.
  • The microbiome makeup is significantly affected both by increasing dietary protein and feeding a raw diet. Although well-documented, the health implications of these changes are not yet completely understood. While some may be considered detrimental (increased risk of certain pathogens), others may come with health benefits, such as an increase of some species found in the family Clostridiaceae. More study is needed on this one.
  • Prebiotics, which are types of fiber that some microbes ferment, can lead to an increase in postbiotics that are associated with health in dogs. However, feeding the correct type of prebiotic, in what type of diet matrix, and at effective (but not too high) levels, remains rather elusive. (Bottom line – if your dog is healthy, he probably does not need a prebiotic; at least until we know more).
  • Ditto on probiotics. While there are some studies showing benefits for dogs with certain forms of GI disease, there are little if any data to support the use of a probiotic with a healthy dog.
  • Your dog’s gut microbiome is important and necessary for his health. Support it by feeding foods that are highly digestible, contain high quality protein, and at least some dietary carbohydrates and fiber. If you feed raw, be aware of potential pathogens in the food (and possibly in feces).

Cited Papers:

  1. Barko PC, McMichael MA, Swanson KS, Williams DA. The gastrointestinal microbiome: A review. Journal of Veterinary Internal Medicine 2018; 32:9-25.
  2. Pilla R, Suchodolski JS. The gut microbiome of dogs and cats, and the influence of diet. Veterinary Clinics of North America: Small Animal Practice 2021; 51:605-621.
  3. Wernimont SM, Radosevich J, Jackson MI, Ephraim E, Badri DV, MacLeay JM, Jewell DE, Suchodolski JS. The effects of nutrition on the gastrointestinal microbiome of cats and dogs: Impact on health and disease. Frontiers in Microbiology 2020; doi:10.3389/fmicb.2020.01266.

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8 thoughts on “Your Dog’s Microbiome – What You Should Know

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  4. Great summary of a complex and emerging area.
    As well as (selectively) eating other animals’ poo, my dog also eats soil, he especially likes the compost I use for potting up plants. I’ve often wondered what these habits are doing for his microbiome. A supplement I give him has Enterococcus Faecium in it. I didn’t see this mentioned above – does it act as a pro-biotic?

    Liked by 1 person

    • Hi Belinda – Yes, Enterococcus Faecium is a probiotic. Is there a reason that you give this supplement? Do you find it helpful for your dog? (We are developing a Science Dog Courses short course on probiotics and will include information about E. faecium in that course!). Thanks for posting! Linda


      • Thanks for your reply. I use something that’s marketed as a calming supplement. It includes tryptophan and glutamic acid but also E. faecium. I think there may be a calming effect though I don’t know what the E. faecium adds, my dog’s digestion has always been pretty robust and doesn’t seem to have changed as a result.


  5. Many dogs forage, eating such tasty things as grass, poo from cats and other species, and roadkill. Has anyone studied whether these act as prebiotics?

    Liked by 1 person

    • Interesting question! Our dogs love to eat grass, rabbit poop, and that really tasty cat poop. And, of course, after eating the poop is when I’m most likely to get a big, wet kiss.


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