Why You Need to Prioritize Your Dog’s Gut Health (And How to Get Started)

May 28, 2024

By Sarah Griffiths, DCH

Over the past 15-20 years, scientists have started down the rabbit hole of trying to create a roadmap of the infinite roles the microbiome has on each body system. We still have a long way to go but many important connections have already been established. From immune-mediated diseases to cancer prevention, understanding the microbiome’s role is crucial for both dog owners and veterinary professionals. Today’s article is focused on the scientifically proven connections between your dog’s gut bugs and the development of common immune-mediated diseases. These established findings demand that we take a different approach for long-term and short term care of our canine family members. Protecting a healthy gut eco system needs to prioritized as we move through various health concerns and life stages of our dog’s lives. Here’s why:

The Gut: A Key Player in Canine Immune Health

The gut microbiome refers to the diverse community of microorganisms residing in your dogs’ gastrointestinal tract. This ecosystem of bacteria, viruses, fungi, and other microbes plays a vital role in maintaining systemic health in dogs. Think of it as an interfacing system between the inside of your dog’s body and the outside world. It allows for accurate discernment in maintaining a healthy system. When it’s healthy, it easily maintains a homeostatic rhythm but it can also cause systemic chaos when it’s damaged. Research has shown that the composition of the gut microbiome directly influences various aspects of canine health, including immune function, digestion, nutrient absorption, and more.

Immune-Mediated Diseases and the Gut Microbiome

Several studies have linked alterations in the gut microbiome (eg. through drastic diet/lifestyle changes or overuse of antibiotics) to the development of immune-mediated diseases in dogs. Conditions such as inflammatory bowel disease (IBD), autoimmune disorders, and allergic reactions have been associated with dysbiosis, an imbalance in the gut microbiota. For example, a study by Suchodolski et al. (2012) found differences in the gut microbiome composition between dogs with IBD and healthy controls, suggesting a potential role of dysbiosis in disease pathogenesis.

Cancer Prevention and the Microbiome

Emerging evidence also suggests a correlation between gut microbiome diversity and cancer prevention in dogs. Certain beneficial bacteria in the gut produce short-chain fatty acids (SCFAs), which have been shown to have anti-cancer properties. Additionally, a balanced gut microbiome can help regulate inflammation and strengthen the immune system, both of which play crucial roles in cancer prevention. A study by Coelho et al. (2020) demonstrated that dogs with a higher diversity of gut microbiota had a lower risk of developing certain types of cancer, highlighting the importance of microbiome health in cancer prevention.

Promoting Microbiome Diversity with Fresh Food Diets

Diet plays a significant role in shaping the composition and diversity of the gut microbiome in dogs. Processed diets high in carbohydrates, containing poor quality proteins and low prebiotic fiber can negatively impact microbial diversity, whereas fresh food diets rich in whole foods can promote a healthier gut microbiome. Raw or lightly cooked meats, fruits, vegetables, and healthy fats provide essential nutrients and support a diverse microbial ecosystem in the gut.

Research on fresh food diets for dogs has shown promising results in promoting microbiome diversity and overall health. A study by Bermingham et al. (2017) compared the gut microbiota of dogs fed a raw meat-based diet to those fed a commercial dry food diet. The results revealed that dogs on the raw meat diet had a more diverse gut microbiome, with higher levels of beneficial bacteria.

The Importance Environmental Diversity

Allowing your dog access to natural spaces is crucial for enhancing gut microbiome diversity. Studies indicate that exposure to diverse environments, particularly those rich in natural elements like soil, plants, and water, introduces a variety of beneficial microorganisms that are otherwise absent in more sanitized, urban settings. A study by Korte et al. (2021) demonstrated that dogs who regularly interacted with natural environments had a significantly more diverse gut microbiome compared to those confined to indoor or urban areas. This increased microbial diversity is linked to stronger immune function and better resistance to pathogens. Additionally, soil-based microorganisms, such as those found in forested areas or parks, have been shown to play a critical role in fortifying the gut microbiome (Reese & Dunn, 2018).

These interactions not only enhance the variety of microbes but also introduce beneficial bacteria that can outcompete harmful ones, promoting a balanced and resilient gut ecosystem. Your dog needs regular access to natural spaces to maintain this. It’s fun and it’s FREE!

Avoiding Unnecessary Antibiotic Use

The overuse of antibiotics in dogs has been shown to have significant and lasting effects on the canine gut microbiome. Research indicates that even a single round of oral antibiotics, such as metronidazole (one of the most common drugs prescribed in veterinary medicine), can lead to profound and long-term alterations in the gut microbiota composition. A study by Pilla et al. (2020) found that the gut microbiome of dogs did not fully recover to its original state even after 18-24 months following antibiotic treatment. This disruption can lead to decreased microbial diversity and an imbalance in beneficial bacteria, potentially contributing to various health issues, including gastrointestinal problems and a weakened immune system. The persistence of these changes highlights the critical need for cautious use of antibiotics in veterinary medicine to preserve the canine gut microbiome (Pilla et al., 2020). Feeding an ultra processed diet and living in a sterilized environment can further exacerbate a long-term microbiome imbalance.


The above facts are just a brief overview of how important it is to preserve and prioritize gut health in dogs. The way that we prioritize care for our dogs needs a major overhaul. The application of new scientific principles is always painfully behind in terms of medical protocols so it’s essential that you do your own research to stay current on the latest findings and to be the authority on decision-making when it comes to your dog’s care. If you can’t make heads or tails of the best options for your dog, get help from an integrative professional.

By understanding the importance of microbiome diversity how to support it, pet parents and veterinary professionals can take proactive steps to enhance the well-being of dogs and help prevent serious illness. As research in this field continues to evolve, we will surely see an increased argument in favour of prioritizing the protection of the canine gut ecosystem.


Bermingham EN, Young W, Kittelmann S, Kerr KR, Swanson KS, Roy NC, Thomas DG. (2017). Dietary format alters fecal bacterial populations in the domestic cat (Felis catus). Microbiome, 5(1), 1-12.

Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR. (2020). Similarity of the dog and human gut microbiomes in gene content and response to diet. Microbiome, 8(1), 1-12.

Suchodolski JS, Dowd SE, Wilke V, Steiner JM, Jergens AE. (2012). 16S rRNA gene pyrosequencing reveals bacterial dysbiosis in the duodenum of dogs with idiopathic inflammatory bowel disease. PLoS One, 7(6), e39333.

Korte, S. M., Bouwman, K. M., van Egmond, D., & Spruijt, B. M. (2021). Environmental enrichment in kennelled dogs: effects of physical activity and spatial complexity on dog behavior and gut microbiome diversity. Applied Animal Behaviour Science, 235, 105236.

Reese, A. T., & Dunn, R. R. (2018). Drivers of microbiome biodiversity: A review of general rules, feces, and ignorance. mBio, 9(4), e01294-18.

Pilla, R., Gaschen, F. P., Barr, J. W., Olson, E., Honneffer, J. B., & Guard, B. C. (2020). Effects of metronidazole on the fecal microbiome and metabolome in healthy dogs. Journal of Veterinary Internal Medicine, 34(4), 1479-1491.