The importance of the microbiome in maintaining good systemic health in companion animals

In recent years we have come to understand that the gastrointestinal (GI) tract is far more than just a digestive organ. The gut is home to a complex ecosystem of trillions of microorganisms known as the gut microbiome, and the microbiome has influence not only digestion, but also to an animal’s overall health, including immune function, skin health, mental well-being, and metabolic balance.

In is therefore understandable that for both dogs and cats, maintaining their gut health is critical. Whereas a healthy gut microbiome has positive effects on an animal’s wellbeing, dysbiosis (an imbalance of the microbiome) can lead to systemic issues such as chronic enteropathies, skin issues, behavioural disturbances, or reduced immunity. Disturbances in the gut environment can arise from diet, stress, antibiotics or disease.

Understanding the gut microbiome

The gut microbiome refers to the trillions of microorganisms, mostly bacteria, but also fungi, viruses, and protozoa, that inhabit the gastrointestinal tract. The microbiome is central to supporting the GI tract both in GI health and digestion. Some of its many roles include:

• Digestive support – The microbiome aids in breaking down food, including fermenting dietary fibres into short-chain fatty acids (SCFAs) and extracting nutrients
• Vitamin synthesis – notably B vitamins and vitamin K
• Barrier protection – The gut microbiome interacts with the epithelium through various mechanisms to maintain intestinal epithelial integrity
• Immune modulation – guiding immune cell development and inflammatory responses. The microbiome also influences the local production of antibodies[i]

While dogs and cats both rely on a balanced microbiome for health, species differences in GI anatomy and diet influence their microbial populations. Cats, being obligate carnivores, have shorter GI tracts and a distinct fermentative capacity compared to more omnivorous dogs.

Several variables can impact the microbiome:

• Diet composition – especially fibre content and protein source
• Medications – notably antibiotics, which can induce dysbiosis
• Life stage – microbiota diversity evolves with age
• Stress and environment – travel, hospitalisation, or boarding can disturb microbial balance

Many diseases, both systemic and localised are associated with imbalanced microbiome, or dysbiosis. Although causation is yet to be proven, and it may be that dysbiosis is a symptom of disease rather than cause, we know that dysbiosis is associated with metabolic diseases, intestinal inflammation, diarrhoea, obesity, cancer, neurologic dysfunctions, poor coat quality, pruritic and many other conditions[ii].

Gut Health and Immunity

Approximately 70–80% of the immune system resides in the gut-associated lymphoid tissue (GALT). This means the GI tract is not only a digestive organ but also a critical hub for immune regulation. Microbial signals help the immune system distinguish between harmless antigens and true threats, shaping the body’s tolerance and inflammatory responses.

Dysbiosis is increasingly linked to chronic diseases in pets:

• Chronic enteropathies (e.g. IBD)
• Dermatological conditions (linked via the gut–skin axis)
• Behavioural changes (via the gut–brain axis)
• Obesity and insulin resistance
• Immune dysregulation, including poor vaccine responses

There are several therapies that can support a healthy balance of the gut microbiome in dogs and cats. The first is nutritional supplementation of probiotics and postbiotics. Probiotics contribute live beneficial microbes to help restore balance within the microflora. Postbiotics are functional metabolic by-products of gut fermentation, and include short chain fatty acids, enzymes and vitamins. Along with pre and probiotics, they help support the microbiome.

Fecal microbiota transplantation (FMT) involves transferring healthy gut bacteria from a donor (healthy) dog to another, compromised dog. It has the potential to transfer an entire ecosystem of flora and should be done under the guidance of a veterinary professional.

Diet underpins a healthy microbiome, and the gut microbiome is extremely sensitive to dietary inputs. Diets rich in fermentable and insoluble fibres, polyphenols, and bioactive compounds can foster positive microbial diversity and function.

Key Dietary Strategies

• Fibre supplementation – both soluble and insoluble forms improve stool quality and promote SCFA production
• Digestive enzymes – enhance nutrient absorption and reduce fermentative burden
• Functional proteins – hydrolysed or novel proteins may reduce GI inflammation
• Polyphenol-rich fruit extracts – provide antioxidant and anti-inflammatory support

The gut microbiome profiles in different species reflect their diet composition, although in dogs the individual ingredients appear to be less important than the overall macronutrient content in terms of influencing the microbiome. Protein, fibre and starch have the most influence on altering the microbiome, however in cases of disease where the level of dysbiosis is high, additions of probiotics can be helpful to improve microbial diversityⁱⁱ.

This concurs with the growing trend in companion animal health with the use of nutraceuticals designed to modulate the microbiome and improve gut function.

Pre-, pro- and postbiotics

Dietary supplementation for GI support now often integrates three classes of bioactive ingredients: Pre, pro and post biotics. Prebiotics are non-digestible carbohydrates that are beneficial ‘food’ for the microbiome. Probiotics are live organisms, primarily bacteria and yeasts that help populate the microbiome, and postbiotics are bioactive compounds produced from probiotic fermentation.

Prebiotics -Fuel for the microflora

• FOS (fructo-oligosaccharides) – stimulate Bifidobacteria and Lactobacilli
• MOS (mannan-oligosaccharides) – help prevent pathogenic adhesion and modulate immune responses
• Beta-glucans – derived from yeast; activate immune cells via Dectin-1 receptors

Probiotics- Live beneficial microbes

• Enterococcus faecium – improves stool consistency and microbial balance
• Lactobacillus acidophilus – supports mucosal immunity and digestion

Postbiotics: Bioactive molecules from non-living microbes

• Include short-chain fatty acids, peptides, and cell wall fragments
• Offer benefits without requiring colonisation
• Strains like L. helveticus, L. paracasei, L. plantarum provide anti-inflammatory and barrier-protective effects

A targeted approach to anal gland health

When we talk about the microbiome it is often when discussing GI health or digestive upset. We also often reference it when linked to systemic issues such as pruritis or even behaviour. The microbiome has a far-reaching influence, and within the digestive system this reaches to the anal glands. Anal gland issues are a frequent concern in small animal practice, particularly in dogs affecting up to 12% of all canines[iii], and occasionally in cats as well. While sometimes dismissed as a minor nuisance, anal gland problems can cause significant discomfort, secondary infection, and contribute to broader gut health challenges.

Anal gland issues are often linked to poor stool consistency or chronic inflammation of the perianal region. Fortunately, most cases of anal gland dysfunction are manageable and often preventable, with a focus on digestive health.

Dietary modification, specifically increased fibre, helps to produce firm well-formed stools which provide the necessary pressure to naturally express the anal glands during defecation, reducing the likelihood of impaction.

Dietary Fibre:

• Helps produce well-formed stools
• A balance of soluble and insoluble fibre promotes both bulk and moisture regulation in stools
• Soluble fibre ferments in the gut to support beneficial bacteria and produce short-chain fatty acids
• Insoluble fibre adds bulk and aids in regular motility

The gut and anal glands are closely interconnected, and a healthy microbiome is essential. To support the microbiome, probiotics can help restore microbial balance, reduce flatulence, and support regular bowel movements, all of which contribute to healthier anal gland function. GlandVet is a nutritional supplement targeted for anal gland health as it contains a balanced amount of fibres and probiotics which supports long-term anal gland function.

GlandVet Composition:

• Insoluble fibre (white oat fibre) – promotes bulky, well-formed stools that naturally express anal sacs
• MOS and beta-glucans – enhance gut immunity and reduce localised inflammation
• Psyllium husk – adds stool moisture and supports motility
• Nucleotides – support mucosal repair and immune cell regeneration
• Fruit extracts – rich in enzymes and polyphenols with anti-inflammatory and digestive benefits
• Probiotics – E. faecium and L. acidophilus to reinforce microbial balance

By improving stool quality and digestive efficiency, GlandVet contributes to a healthier gut environment and more consistent, natural expression of anal glands. This makes it suitable for dogs with recurrent impaction or inflammation.

From GI health to whole-body benefits

Whether addressing chronic diarrhoea, food sensitivity, post-antibiotic recovery, or anal gland dysfunction, supporting gut health should be a core part of the therapeutic strategy.

Recommendations for practice:

• Choose evidence-based supplements with defined ingredients and strain-specific probiotics
• Assess stool quality, frequency, and composition as key indicators of GI health
• Tailor fibre type and source to individual patient needs

Integrate nutraceuticals like GlandVet alongside dietary and medical management. The GI tract and its microbial inhabitants influence far more than digestion—they shape immune responses, inflammation, skin integrity, behaviour, and even glandular function. By investing in gut health through targeted, evidence-based supplementation, vets can support their patients’ resilience from the inside out.

With advanced products like GlandVet, we can now deliver multi-dimensional support for gut health, addressing a wide spectrum of clinical needs through a nutraceutical lens. In doing so, we help redefine what preventive and integrative care looks like for modern companion animals.

References:

Toresson, L., Suchodolski, J. S., Spillmann, T., Lopes, B. C., Shih, J., Steiner, J. M., & Pilla, R. (2023). The intestinal microbiome in dogs with chronic enteropathies and cobalamin deficiency or Normocobalaminemia—A comparative study. Animals (Basel), 13(8), 1378. https://doi.org/10.3390/ani13081378

Pilla, R., Guard, B. C., Blake, A. B., Ackermann, M., Webb, C., Hill, S., Lidbury, J. A., Steiner, J. M., Jergens, A. E., & Suchodolski, J. S. (2021). Long-term recovery of the fecal microbiome and metabolome of dogs with steroid-responsive enteropathy. Animals (Basel), 11(9), 2498. https://doi.org/10.3390/ani11092498

Schmidt, M., Unterer, S., Suchodolski, J. S., Honneffer, J. B., Guard, B. C., Lidbury, J. A., Steiner, J. M., Fritz, J., & Kölle, P. (2018). The fecal microbiome and metabolome differs between dogs fed Bones and Raw Food (BARF) diets and dogs fed commercial diets. PloS one, 13(8), e0201279. https://doi.org/10.1371/journal.pone.0201279

Baglama, S. S., & Trcko, K. (2022). Skin and gut microbiota dysbiosis in autoimmune and inflammatory skin diseases. Acta Dermatovenerologica Alpina, Panonica, Et Adriatica, 31(3), 105-109. https://doi.org/10.15570/actaapa.2022.16

Fritsch, D. A., Jackson, M. I., Wernimont, S. M., Feld, G. K., Badri, D. V., Brejda, J. J., Cochrane, C. Y., & Gross, K. L. (2023). Adding a polyphenol-rich fiber bundle to food impacts the gastrointestinal microbiome and metabolome in dogs. Frontiers in veterinary science, 9, 1039032. https://doi.org/10.3389/fvets.2022.1039032

Lappin, M. R., Zug, A., Hovenga, C., Gagne, J., & Cross, E. (2022). Efficacy of feeding a diet containing a high concentration of mixed fiber sources for management of acute large bowel diarrhea in dogs in shelters. Journal of Veterinary Internal Medicine, 36(2), 488-492. https://doi.org/10.1111/jvim.16360

Benyacoub, J., Cavadini, C., Sauthier, T., Schiffrin, E. J., von der Weid, T., Czarnecki-Maulden, G. L., & Anderson, R. E. (2003). Supplementation of food with enterococcus faecium (SF68) stimulates immune functions in young dogs. The Journal of Nutrition, 133(4), 1158-1162. https://doi.org/10.1093/jn/133.4.1158

Kiełbik P, Witkowska-Piłaszewicz O. The Relationship between Canine Behavioral Disorders and Gut Microbiome and Future Therapeutic Perspectives. Animals (Basel). 2024;14:2048.

Dewey, C. W. (2025). Poop for thought: Can fecal microbiome transplantation improve cognitive function in aging dogs? Open Veterinary Journal, 15(2), 556-564. https://doi.org/10.5455/OVJ.2025.v15.i2.6