The gut microbiome
Understanding and supporting the gut microbiome isn’t a fringe interest: it’s fast becoming a core part of modern canine care.
Once regarded as the body’s digestive assistant, the gut microbiome is now recognised as one of the most important influences on overall health, in us and our dogs. With its trillions of microorganisms (mainly bacteria, but also fungi, archaea, protozoa and viruses), this dynamic, interactive organ is a natural barrier that wards off pathogens, supports digestion and is inextricably linked to health and wellbeing.
Oh, and although we’re talking specifically about the gut here, the microbiome isn’t limited to the gut: other sites include the skin, ears, eyes, urinary tract and respiratory tract[1].
So, some knowledge of the microbiome is useful not only for keeping our dogs healthy but also to help us guard against allergies, intestinal conditions and obesity. Fortunately, there is plenty of canine research to draw on.
This series of articles will look more closely at the canine gut and the relationship between diet, nutrition and health, citing the relevant studies where appropriate.
What is the gut microbiome?
The gut microbiome is the environment or ecosystem in the gastrointestinal tract, particularly the colon, where the microbial communities live. A healthy microbiome supports digestion, of course. But it performs many other functions – in fact, gut health plays an astonishingly wide role in maintaining canine health. Some of its most vital functions include:
- Immune modulation: up to 70% of the immune system resides in the gut-associated lymphoid tissue (GALT), meaning the microbiome has direct influence over immune education and inflammatory response.
- Skin and allergy health: evidence is growing that gut imbalance can precede or exacerbate skin conditions like atopic dermatitis. A 2023 study[2]demonstrated that dogs with atopic dermatitis had significantly different gut microbiota profiles compared to healthy dogs. They also highlighted that diet and prior antibiotic exposure were key factors in shaping this microbial landscape, underscoring how lifestyle choices affect immune-related conditions.
- Nutrient metabolism: microbes contribute to the breakdown of fibre and complex carbohydrates, producing short-chain fatty acids (SCFAs) that nourish intestinal cells and regulate inflammation.
- Protection against pathogens: a diverse microbiota helps prevent colonisation by harmful microbes. A healthy gut can even affect recovery from the use of antibiotics. Omega-3 fatty acids, for example, can help restore balance and microbial diversity.
- Communication with the brain: through the gut–brain axis, microbial activity can influence behaviour, stress response, and mood (more on this in a future article).
Dysbiosis: when things are out of sync
Gut dysbiosis occurs when there is an imbalance in the microbiome. It can result from an existing condition and/or create additional problems. For example, dysbiosis can set the stage for systemic issues such as gastrointestinal disorders, chronic inflammation, IBS and allergic responses, which in turn can also lead to mood or behavioural shifts in our dogs. Poor diet is one thing that can cause this disruption.
Signs of gut dysbiosis in dogs can be subtle or systemic, and may include:
- Chronic diarrhoea or soft stools
- Loss of weight or inability to gain weight
- Recurrent ear or skin infections
- Flatulence, bloating, or stomach gurgling
- Itchy skin without obvious external cause
- Poor response to common allergy treatments
A happy gut: the effect of diet
Diet is one of the most powerful tools we have for shaping our dog’s gut microbiome. Different macronutrient profiles – especially the balance between protein, fibre and carbohydrates – can significantly alter the composition and metabolic activity of gut bacteria.
So, if we want to optimise ingredients and diet for our dogs, it’s helpful to understand the role of digestion and the gut microbiome in the relationship between food and health.
Basically, high-protein, low-carbohydrate diets are often associated with increased bacterial diversity and a higher abundance of beneficial genera. Diets rich in fermentable fibre can promote short-chain fatty acid (SCFA) production, supporting colonocyte health and modulating inflammation.
Conversely, ultra-processed or carbohydrate-heavy commercial diets tend to reduce diversity, potentially leading to overgrowth of less beneficial species. The inclusion of synthetic additives and a lack of dietary variety may further contribute to dysbiosis.
Supporting a healthy gut begins with feeding a balanced, species-appropriate diet, remembering that dietary change should be made gradually and, where there are pre-existing conditions, with the advice of a specialist. Healthy ingredients may include single high-quality animal proteins, low-starch vegetables, as well as plant-based sources of dietary fibre and nutrients. Fermented foods are also on the list, although they’re not always tolerated, so be careful!
Other factors
In dogs, the composition and diversity of this microbial population are influenced by several factors, including:
- early-life exposures (birth method, maternal microbiota, weaning practices)
- environment and hygiene
- diet composition and feeding patterns
- lifestyle (rural or urban)
- antibiotic use or overuse
- age, breed, and body condition score.
A 2021 study[3] compared the gut microbiota of 96 healthy dogs and found that breed, age, and body condition score (BCS) all played a role in shaping microbial communities.
For example, younger dogs typically showed a higher proportion of fast-growing bacteria, while older dogs exhibited more diversity among fibre-degrading species. Breed-related factors influenced microbial richness and dominance of specific taxa.
These findings are important because they caution against overinterpreting variation: a dog’s microbiome will naturally reflect their physiology and lifestyle. The focus should be on overall diversity and preventing harmful dysbiosis patterns, not rigid ideas of what a ‘healthy’ microbiome must look like.
Start the reset!
The gut is far more than a digestive organ: it’s a control centre that shapes a dog’s immune function, skin health, nutrient absorption and even behaviour. A growing body of research shows that by understanding and supporting the microbiome, we can improve not only digestive wellbeing, but the overall health and resilience of our dogs.
Remember, we’re not just looking after one dog. We’re looking after millions of the organisms they carry around with them!
If we keep them happy, the rest will follow.
This article has also been published on Substack at https://doggydellycom.substack.com/p/happy-and-healthy-dogs-gut-health.
References
[1] Pilla R, Suchodolski JS. (2020). *The Role of the Canine Gut Microbiome and Metabolome in Health and Gastrointestinal Disease*. Frontiers in Veterinary Science. https://doi.org/10.3389/fvets.2019.00498
[2] Sinkko H, Lehtimäki J, Lohi H, Ruokolainen L, Hielm-Björkman A. (2023). *Distinct healthy and atopic canine gut microbiota is influenced by diet and antibiotics*. Royal Society Open Science. https://doi.org/10.1098/rsos.221104
[3] You I, Kim MJ. (2021). *Comparison of Gut Microbiota of 96 Healthy Dogs by Individual Traits: Breed, Age, and Body Condition Score*. Animals. https://doi.org/10.3390/ani11082432