Last Updated: 26/02/2026
Improve Pet Gi Health Using The Microbiome
Did you know your pet's gut is home to trillions of tiny organisms? Discover how the microbiome influences everything from digestion to immunity, and learn how prebiotic-rich diets can help your dog or cat by balancing their gut health.
Author: Dr Teagan Lever BVSc (Hons)
Reading Time: 4 minutes - short read
While we often focus on what goes into a pet’s bowl, it is what is happening inside their digestive tract that truly dictates their wellbeing. The gut microbiome - a complex ecosystem of bacteria and fungi - acts as a hidden engine for health. When this system is in balance, pets thrive; when it’s not, issues like flatulence, upset stomachs, and irregular stools become the norm. Understanding how to nourish these beneficial "bugs" is the secret to supporting a happy, healthy pet from the inside out.
Pet microbiome basics
What is a microbiome?
The word microbiome is esentially just a fancy science word which refers to the communities of microorganisms (bacteria, fungi and more) which live in a particular environment, including on (and in!) humans and animals.
In many cases, research into the human and animal microbiome has focused on the microbiome of the gut - that is the tiny little organisms which live in the intestinal tract. For a long time we have understood that having the right balance of these little critters can play an important role in digestive health; this is the reason your doctor may recommend to take probiotics after a course of antibiotics.
So what's new?
In 2007 the US National Institutes of Health (NIH) launched the Human Microbiome Project, using genetic sequencing technology to develop an understanding of what bacterial (and other) species inhabit 5 areas of the body (including the gut) and how they change in certain disease states such as inflammatory bowel disease or pre term birth.
Among the findings of the decade of research that went into this project was that in some health conditions, including inflammatory bowel disease, there are changes to the types and behaviours of the microorganisms present. Further research into the human and animal gut microbiome has found that there are also differences present in the gut microbiome in many other disease processes including kidney failure, obesity and even mental health conditions.
How does this apply to my pet?
Now that we know there is a link between what the microbiome in the gut is doing and digestive health, as well as other parts of the body, the next step is figuring out how use the power of science to manipulate the microbiome for good. And there are a lot of ways that the microbiome can be altered to help improve health. Interventions aimed at the gut microbiome might be aimed at increasing the diversity of bugs that are there, or in other cases encouraging the growth of certain species known to be present in healthy pets
When it comes to manipulating the gut microbiome, faecal transplants stand out as a success story. It sounds gross, but stick with me here. Essentially many humans (and pets) have been successfully treated for a range of digestive tract issues by simply transplanting the faeces (yes poo!) from a healthy donor into the gut of the patient. And it works!
So next time you catch your pooch with their head in the kitty litter, maybe it's just their way of increasing the diversity of their gut microbiome with a DIY faecal transplant!
How does the microbiome impact digestive health?
Dysbiosis refers to an imbalance between the desirable and undesirable bacteria within a microbiome.
In the microbiome of the gut, dysbiosis can result in a range of digestive symptoms such as diarrohea, constipation, flatulence, decreased appetite and nausea. Dysbiosis can be triggered by a range of factors including genetics, diet, stress, antibiotics and infectious organisms.
With this in mind, it makes sense that establishing and maintaining populations of desirable bacteria in the gut is an important part of treating gastrointestinal diseases in our pets.
How food can be used to harness the power of the microbiome
When it comes to trying to influence the microbiome to improve health, traditionally in both human and animal medicine there has been a focus on probiotics. That is, trying to establish populations of known beneficial bacteria in the gut by consuming live organisms in supplements or food. While this may improve symptoms in some cases, there is a not a lot of hard evidence supporting the use of probiotics to treat digestive illness in pets.
New research has highlighted that prebiotics, substances which promote beneficial gut bacteria, like dietary fibres, have an important role to play in the health of the gut microbiome and the digestive tract in general.
Feeding a diet enriched with certain prebiotic dietary fibres has been demonstrated to positively influence the health of the microbiome in dogs and cats with digestive disorders.
Prebiotic fibres are fermented by beneficial bacteria, producing gut nourishing compounds and resulting in the release and activation of, micronutrients with antioxidant and anti inflammatory effects, positively impacting gut health. These beneficial products of desirable bacteria are called postbiotics. In addition, by feeding the beneficial bacteria, the growth of potentially undesirable bacteria is also reduced.
Using the power of the microbiome to help manage digestive health problems is a new area in pet nutrition, and the Hill's Prescription Diet Gastrointestinal Biome range is designed for this purpose.
Hill's Prescription Diets are specially formulated for the management of specific health conditions and are not suitable for all pets. Please check with your veterinarian prior to changing your pet's diet.
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History
Our experts continually monitor the health and wellness space and we update our articles when new information becomes available.
Thu 26 Feb 2026
Edited by Dr Gillian Hill BVSc (Hons)Dr Teagan Lever BVSc (Hons)
Head Veterinarian, BVSc (Hons)
Pet Circle's Head Veterinarian, Dr Teagan graduated from the University of Queensland in 2010 and went on to work in small animal and mixed practice in various locations around QLD & ACT before joining Pet Circle in early 2016. Dr Teagan has special interests in dermatology, nutrition and preventative health care. She feels privileged to witness the special bond people share with their pets on a daily basis and enjoys forming lasting relationships with pet parents and their fur children.
