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What is the Gut Microbiome?

And more importantly, why does it even matter?

Most dogs will suffer from digestive issues at some point, just like humans might. Parasites picked up outside can lead to common ailments, such as giardia, that lead to pretty nasty symptoms, including diarrhea, vomiting, excessive gas, weight loss, and loss of appetite. Fortunately, this common issue is identified by a simple stool test from your vet and remedied by oral dewormers.

However, there are also many other causes — anxiety, stress, sudden changes in diet, antibiotics, and sensitive digestive tracts — and the unfortunate reality that dogs can’t tell us what’s wrong. Like many attentive dog parents, we found ourselves constantly managing symptoms.

We were both stressed out by the perpetual guessing game and lack of understanding. How could science and technology advance so many aspects of our lives, yet we were still playing whack-a-mole? Already familiar with the advancements in understanding the role of humans’ microbiome, we believed there could be similar concepts with our dogs’ health.

But, what is the microbiome? Perhaps this word sounds vaguely familiar? It is frequently discussed in the science community, sometimes under the sometimes under the term microflora, which only partly describes the amazingness of what makes up microbiomes!

In general, the microbiome refers to the ecosystem of bacteria and other microorganisms living on or inside an animal. There can be many microbiomes in a single animal, including the gut, skin, and mouth. Both humans and dogs have microbiome communities like this! The microbiome is extremely complex, and the source of both emerging and ongoing research.

Three of our favorite facts about the canine gut microbiome include:


  1. Over 70% of dogs’ immune system can be found in their digestive tract where key functions are performed, including preventing the growth of disease causing pathogens like E. coli and Salmonella.

  2. Puppies are born without a microbiome and inherit their biodiversity as they drink their mother’s milk.

  3. Without the microbiome, dog’s digestive tracts would not be able to process essential vitamins and minerals.

The BarkBiome Project’s focus is on advancing our understanding of dogs’ gut microbiome given the foundational role it plays in their overall wellbeing. Trillions of bacteria and microorganisms reside along the digestive tract which has metabolic functions such as producing essential nutrients, but has also been linked to other conditions such as aggression and anxiety. Each dog’s gut microbiome is extremely unique and is impacted by variations in elements such as diet, antibiotics, exercise, genetics, age and other hygiene and environment factors.

The highest concentration of bacteria is found in the gut, specifically the intestines, where they perform important digestion tasks. These bacteria can be either good or bad (though similar to anything in nature, the imbalance of too much or too little of something can have negative effects). The good guys, known as probiotics, aid in breaking down macronutrients, like protein and fiber, as well as absorbing and producing needed vitamins. Since the average dog digests food much faster than a human (approx. 6–8 vs. 20–30 hours, respectively), it is important that there are ample probiotics to enable vital nutritional intake.

Although the microbiome is ever-changing, when it is negatively disrupted or damaged, the consequences can be significant. Some of the potential symptoms that have been connected to damaged microbiomes include food allergies, weight gain, chronic inflammation, mood disorders, diarrhea, constipation, irritable bowel syndrome, and more.

Since the microbiome is constantly evolving, there are ways to help proactively support and nurture your dog’s gut, and total wellness, such as:


  1. Including fresh foods that naturally contain bacteria, like kefir

  2. Introducing probiotic supplements to your dog’s care routine

  3. Avoiding highly processed diets, like kibble, when possible (Given probiotics are living organisms, they’re extremely sensitive to the high temperatures of dry food manufacturing. Unfortunately, they rarely survive the process and make it into your dog’s bowl.)

By analyzing each dog’s unique microbiome composition, the BarkBiome Project aims to understand our dogs’ health through cutting-edge science and analytics so that better solutions are available for pet parents in the future!

Think your dog would be a great canine citizen scientist at the BarkBiome Project? Contact us!