Nurturing Your Pet’s Microbiome

By Stephen T. Sinatra, M.D., F.A.C.C., F.A.C.N., C.N.S., C.B.T.

When you became a dog or cat owner, I bet you never thought he or she would come with a whole community of other bugs as part of the package.

Fortunately, I’m not talking about fleas, ticks, or mites. I’m talking about your pet’s microbiome. And unlike fleas and other pests, the “bugs” that make up the microbiome serve an important purpose in the health of your furry friend.

What is the Microbiome?

Like humans, dogs and cats have a vast collection of microorganisms that reside on and in their bodies. Thousands of different species of bacteria, viruses, fungi, archaea, and protozoa—totaling trillions of microbes—make up the microbiome. While the largest numbers are found in the gastrointestinal tract (the “gut”), they exist all over—on the skin, in the mouth, nose, and ears, and in internal organs.

All of these microbes play a role in the health of your dog or cat. In fact, researchers now consider the microbiome a “metabolically active organ inextricably linked to pet health.”1

According to a 2019 study, these are just a few of the critical roles spearheaded by the canine gut microbiome:

The gut microbiome contributes with metabolic functions, protects against pathogens, educates the immune system, and, through these basic functions, affects directly or indirectly most of our physiologic functions. Serotonin, a neurotransmitter, is mostly produced in the intestine… A healthy and stable microbiome can simultaneously act as pro- and anti-inflammatory, keeping a balance to prevent excessive inflammation while still being able to promptly respond to infections.”2

Microbiome Balance Vs. Dysbiosis

Considering all the good the microbiome does, you’d think the “bugs” that comprise it are all beneficial and “friendly” in nature. But in reality, the microbiome consists of microbes that are both helpful and potentially pathogenic. In a healthy dog or cat, the good and bad guys coexist peacefully and balance each other out, which prevents harmful ones from taking over.

But if that delicate balance is disturbed, the bad guys can gain a stronghold—a condition called dysbiosis. This often contributes to intestinal inflammation, leaky gut, and increased risk of illness and disease.

Any number of things can disrupt microbiome balance. In dogs and cats, the top offenders are:

  • Abrupt diet change/dietary indiscretion
  • Parasites
  • Improperly balanced diet
  • Antibiotics
  • Stress

Exposure to harsh chemicals like glyphosate (a main ingredient in household weed killers and a common herbicide used in conventional farming) may also impact a pet’s microbiome. Various studies link exposure to pesticides with dysbiosis in hosts such as mice and fish, but more research is needed to confirm a negative impact on the gut microbiome of dogs and cats. 3-4

Just as is the case in humans, dysbiosis in dogs and cats may be associated with other health conditions:5

  • Digestive disorders (gas, bloating, leaky gut, inflammatory bowel disease, diarrhea, vomiting, or abdominal pain)
  • Obesity
  • Bad breath
  • Infections
  • Weakened immune system
  • Skin allergies
  • Joint pain
  • Gum disease

How to Support Your Pet’s Microbiome

The good news is, restoring your dog’s or cat’s microbiome isn’t all that difficult. Here are the three main things to do.

Change Your Pet’s Diet

Adjusting your dog’s or cat’s diet can go a long way to correcting microbiome imbalances.

According to a 2020 study:

Food serves as a substrate for the GI microbiome of cats and dogs and plays a significant role in defining the composition and metabolism of the GI microbiome. The microbiome, in turn, facilitates … nutrient digestion and the production of postbiotics, which are bacterially derived compounds that can influence pet health. Consequently, pet owners have a role in shaping the microbiome of cats and dogs through the food they choose to provide.”1

Indeed, providing the best food possible is one of your most critical roles as a pet owner.

Cats’ diets are pretty clear-cut—they are carnivores, plain and simple. They can tolerate a vegetable or carbohydrate here and there, but their primary source of food should be meat-based. Straying from this too much can lead to dysbiosis.

Dietary ratios for dogs are a little looser. They can handle carbohydrates and can even survive on them if necessary, but proteins are definitely preferred for better microbiome balance.

Case in point: A 2017 study involving 32 labs and 32 beagles found that those that ate the high-carb/low-protein diet for four weeks experienced major microbiome changes, including elevated levels of bacteria associated with obesity. On the other hand, the dogs on the high-protein/low-carb diet had greater amounts of bacteria typically seen in leaner dogs.6

Research has shown that a raw food diet supports a healthier microbiome in dogs. One study found that dogs given a raw diet had an abundance of bacteria necessary for a healthier gut, compared to dogs on dry kibble.7

Even so, raw diets remain controversial and many dog owners prefer not to take any chances. In these cases, I recommend the addition of freeze-dried foods (which can be offered to both dogs and cats). These are minimally processed and made with raw animal proteins, and the freeze-drying process allows for retention of nutrients with far less risk of bacterial contamination. This makes freeze-dried food an excellent alternative to raw food—all the benefits with fewer concerns.

Additionally, you can still feel confident feeding your dog kibble if you read the ingredient label carefully and choose a high-quality, organic brand. This helps ensure the meats were sourced from antibiotic-free livestock that were fed non-GMO feed. (Remember, antibiotics are major microbiome disrupters and GMO foods are often produced using toxic pesticides, which may impact microbiome health.)

Add Probiotic Supplements

The second most important thing you can do to support your pet’s microbiome is to provide probiotics. Probiotics supplements are literally beneficial (“pro”) bacteria (“biotics”). Taking probiotics can help your dog or cat in several ways, including:

  • Better balance of bacteria in the gastrointestinal tract, which promotes healthier digestion
  • Maintaining proper gut pH
  • Stronger immune system function

Overall, a healthier gut means better ability to break down food and absorb nutrients, and less risk of gastrointestinal upset.

If your cat is an adventurous eater (because let’s face it, dogs will eat anything…), try offering probiotic-rich “human food.” Many cats enjoy plain yogurt, which naturally contains probiotic cultures. Buy a brand made of nothing but milk and probiotics—the more strains, the better. And this is the only dairy your cat should be allowed, as other milk products tend to have the opposite of the desired effect!

Dogs can eat a wider variety of fermented foods, but be sure to give them gradually so they don’t experience digestive issues like gas or bloating. Different options for dogs include yogurt, buttermilk, cheese, sauerkraut, kimchi, and whey.

Avoid Pesticides & Drugs

Finally, do your best to avoid the unnecessary use of drugs. If possible, find natural ways to prevent fleas and ticks. Give antibiotics or other medications only if absolutely necessary. Avoid using glyphosate and chemical pesticides/fertilizers in your own yard, opting instead for safer, more natural alternatives.

It’s impossible to completely avoid these chemicals since they’re so ubiquitous in our society, but do what you can to provide the safest environment possible.

It doesn’t happen overnight, but by making the following changes, additions, or switches in your dog’s or cat’s diet/lifestyle, his/her gut will slowly start becoming more balanced, and better health will be restored.

*This blog was developed with Veterinarian Dana Wilhite, DVM to help educate pet owners.


  1. Wernimont S, et al. The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease. Front Microbiol. 2020 Jun 25;11:1266. doi: 10.3389/fmicb.2020.01266.
  2. Pilla R and Suchodolski J. The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease. Front Vet Sci. 2019;6:498.
  3. 3.  Zhou, Meng, and Jiang Zhao. “A Review on the Health Effects of Pesticides Based on Host Gut Microbiome and Metabolomics.” Frontiers in molecular biosciences vol. 8 632955. 8 Feb. 2021, doi:10.3389/fmolb.2021.632955
  4. Rueda-Ruzafa L, Cruz F, Roman P, Cardona D. Gut microbiota and neurological effects of glyphosate. Neurotoxicology. 2019 Dec;75:1-8. doi: 10.1016/j.neuro.2019.08.006. Epub 2019 Aug 20. PMID: 31442459.
  5. Honneffer, Julia B et al. “Microbiota alterations in acute and chronic gastrointestinal inflammation of cats and dogs.” World journal of gastroenterology vol. 20,44 (2014): 16489-97. doi:10.3748/wjg.v20.i44.16489
  6. Li Q, et al. Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions. mBio. 8:e01703-16. DOI: 10.1128/mBio.01703-16.
  7. Sandri M, et al. Raw Meat Based Diet Influences Faecal Microbiome and End Products of Fermentation in Healthy Dogs. BMC Veterinary Research. 2016;13(65).

© Stephen Sinatra, MD. All rights reserved.

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