Just like humans, our cats and dogs also have a gut microbiome. And just like us, their microbiome affects their health. Yet our pets never wash their hands, never bathe daily, and they don’t choose their food independently. It is well recognized that a higher diversity in the gut microbiome means better health. So, in this article, we're going to explore the microbiome of our pets, how nutrition affects their microbiome and how their microbiome influences ours.

Cat and dog microbiome overview

It has been suggested that cats and dogs represent a good model for understanding relevant microbes in the gut microbiome compared to humans because our pets have shorter intestines and a quicker transit time for stool generation. These characteristics makes it easier to follow the gut microbiota in pets.

Cats and dogs share similar bacterial communities like Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, and Actinobacteria.

In general, it has been reported that the gut microbiota composition is similar between cats and dogs. However, different studies show slight differences between dogs and cats, particularly at the level of alpha and beta diversity.

The alpha and beta diversity measurements reflect the richness and/or evenness of the distribution of bacterial groups within and between bacterial communities, respectively (Wernimont et al., 2020).

Alpha v beta diversity

For example, a recent large study with 192 dogs and 46 cats exhibited that higher alpha diversity was found in cats compared to dogs.

Bacterial genera abundant in dogs (Jha et al., 2020):

  • Enterococcus
  • Fusobacterium
  • Megamonas
  • SMB53
  • Adlercreutzia
  • Alistipes
  • Bifidobacterium
  • Carnobacterium
  • Collinsella
  • Coprococcus
  • Desulfovibrio
  • Faecalibacterium
  • Oscillospira
  • Parabacteroides
  • Peptococcus
  • Peptostreptococcus
  • Ruminococcus
  • Slackia
  • Sutterella

Bacterial genera abundant in cats (Jha et al., 2020):

  • Adlercreutzia
  • Alistipes
  • Bifidobacterium
  • Carnobacterium
  • Collinsella
  • Coprococcus
  • Desulfovibrio
  • Faecalibacterium
  • Oscillospira
  • Parabacteroides
  • Peptococcus
  • Peptostreptococcus
  • Ruminococcus
  • Slackia
  • Sutterella

cat vs dog microbial distribution

Nutrition effects on our pets’ microbiomes

Every time we feed our pets, we also feed their gut microbiome. And it is well recognized that the diet has a huge impact in building the gut microbiota (Leeming et al., 2019).

We invite you to check our GoldBio article ¨What gut microbes eat¨ to learn more about the importance of the diet in the gut microbiome.

Most kibble has similar components, proteins, carbohydrates, and fats. Although minimal information about these components is available in pet studies. Therefore, I’ll present what is currently known.


Common fiber foods providing carbohydrates used in the pet food industry include beet pulp, corn, fruit, rice, oat, and barley fiber.

Studies of carbohydrates on microbiome composition evaluated in healthy cats and dogs demonstrated that increasing concentrations of potato fiber, composed of both resistant and digestible starch, increased the proportion of Faecalibacterium in the microbiome.

Also, food with fructooligosaccharides (FOS) increased dogs' beneficial Lactobacillus and Bifidobacterium populations. A FOS can be defined as many sugar molecules joined together. And foods like bananas, onions and wheat have these types of polymer of sugars.

Another study in cats showed that FOS, galactooligosaccharides (GOS), short-chain FOS and GOS- supplemented diets significantly increased Bifidobacterium spp. concentrations, which is a positive bacterial genus (Wernimont et al., 2020).

Interestingly, new sources of fiber such as cricket meal are being studied in pets.

In one study, 32 beagles were fed with diets with a 24% replacement with cricket meal. Authors found that diets containing cricket supported the same level of gut microbiome diversity as a standard healthy balanced diet. In this sense, future novel food ingredient using crickets could support potential health for dogs (Jarett et al., 2019).


Protein is essential to pet food. Studies have been done comparing commercial kibble and raw meat-based diets (RMBD).

Raw meat-based diets are diets based on fresh uncooked meats and includes bones, and residual meat parts of the livestock industry.

Studies have compared differences between RMBD pet food and traditional pet foods and found inconsistent results.

While in dogs, there was higher diversity in their microbiomes with RMBDs, in cats, different taxa were abundant depending on the diets (Wernimont et al., 2020).

However, in both cases, the authors pointed out pets fed with RMBDs may have a greater risk of opportunistic infection than those fed commercial foods.


Regarding fats, most of the studies have been carried out in humans or mice, so the information is scarce for pets.

However, based on the previous studies on the effect of high-fat diets on the detriment of the microbiota (notably decreasing beneficial short fatty acids), it has been proposed that this information could help to define a successful strategy to influence the production of fatty acid postbiotics with the potential to improve obese pets.

The pet microbiome and us

The hygiene hypothesis establishes that exposure to a little dirt early in life can ward off allergies that can appear later.

As we've become more accustom to daily cleaning and sterilization, researchers proposed these higher standards led to a rise in allergic diseases.

Furthermore, it is also known that the human gut microbiome is formed early in life, and our immune system strengthens as we grow.

Billions of microbes reside on and in our pets, including their skin and digestive tracts. What that means for us is that our pets' microbes can be a source of that “little dirt” we all need in early life to improve our immune systems.

Investigators collected information on one million children born in Sweden between 2001 and 2010. From these, a cohort of 275,000 school-age children dog owners had a 13% lower chance of developing asthma than their peers who grew up without a dog (Gupta, 2017).

Furthermore, other studies showed that three-month-old infants with pets had higher microbial richness than those without pets.

Families with pets had higher Ruminococcus and Oscillospira, two types of Firmicutes health-related microbes.

These two taxa have been associated with a lower risk of allergic disease and leanness, respectively (Gupta, 2017).

These studies show us that our pets can serve as microbial transfer agents.

baby with puppy

Altogether, the association between pets, babies, and human health has led us to think very creatively, and ask questions such as:

  • Could we get dog microbes in a pill form?
  • Could we get the microbial world of our pets as a spray?
  • Should doctors recommend children spend time with pets to prevent future illness.

Now there is more evidence that pets play a significant role in our lives when it comes to health and disease.

Pet diseases and gut microbiome

We suffer when our pets are sick. New studies are focusing on understanding the associations between pet diseases and their microbiome composition.

Common pet diseases like chronic enteropathy (CE), allergies, constipation, oral diseases, and obesity are being analyzed in cats and dogs.

Among them, oral issues affect 76% of dogs and 68% of cats. And 60% of cats and 56% of dogs in the United States are overweight or obese (Wernimont et al., 2020).

Most of these diseases show changes in the pet gut microbiomes by reducing the levels of health-related metabolites like short fatty acids, which are a byproduct of bacterial fermentation in the intestines. In other cases, health-related microbiota is reduced.

To overcome these problems, veterinarians are looking for options using prebiotics and probiotics in pet diets.

Prebiotics are nondigestible food ingredients that stimulate the growth of beneficial bacteria in the colon.

Probiotics have been defined as live microorganisms that may confer a health benefit on the host when consumed in adequate amounts.

Reports using probiotics like Lactobacillus rhamnosus or mixtures of commercial strains like SLAB51 have shown positive effects against allergy and constipation, respectively (Wernimont et al., 2020).


The focus of microbiome research has shifted from understanding the impact of compositional changes to how functional changes mediated by nutrition may enhance overall pet health. Therefore, it has been projected that coming microbial research will provide significant benefits for our best friends and pet's owners.


Pet microbiome, pet nutrition, pet health


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