Pet microbiomes and gut health, explained

You may have heard of microbiomes, since it’s been a hot topic in human health for a while. In simple terms, microbiomes are the microorganisms that live in our bodies - anything from bacteria and viruses to even fungi and archaea. Usually, in the right amounts, it’s a symbiotic relationship; we help them a little, then they help us a lot. There are ways to care for your microbiome, and, typically, a well-functioning microbiome is linked with better health, like digestion. Naturally, since we care about our pets so much, we’re concerned about their microbiome performance, too. After all, better health, better digestion and a happier pet sounds good to us. Here, we break down what a pet’s microbiome is, why it’s trending and ways you can support your pet’s helpful community of microscopic critters. Pet microbiomes - at a glance What's a pet’s microbiome, and why should we care? A pet’s microbiome is an ecosystem of microorganisms. They perform various roles, like helping digestion, regulating the immune system, helping absorb nutrients and supporting our pets’ mental health. Our pets host an incredible amount of microbial cells ( between 10^13 and 10^14 microbial cells to be exact ) from over 1,000 bacterial species. While the gut holds the largest amount of these, others live on the skin, mouth and respiratory tract. These microorganisms help our pets do jobs they can’t do alone, like: There’s a lot of science there, but the main thing to remember is this: a pet’s microbiome is important to maintain their health, optimise their nutrition, manage disease and, in some cases, help veterinary professionals diagnose problems. What changed in 2026? This year, scientists published the most comprehensive catalogue of pet gut microbiomes called the “ Waltham catalogue for the canine gut microbiome ”. The team found 5,753 bacterial genomes with 1,031 distinct strains, which was the biggest analysis on record of pet microbiomes. The study found: What does this mean for me and my pet? The end of "human-based" probiotics What’s changed: Previously, pet supplements were largely based on human gut science. But recent research, like the 2026 study we mentioned, has shown that pet microbiomes are substantially different. What this means for you: Expect to see a new generation of pet-specific probiotics that actually contain the bacteria pets naturally need, rather than just "repurposed" human versions that might not survive or thrive in a dog's gut. Vet diagnostics may now be more accurate What’s changed: A greater understanding of pet microbiomes now means vets can understand more about potential problems in your pet’s gut. What it means for you: Vets may soon be able to use more precise "microbiome tests" to see exactly what’s missing or overgrown in your pet. This moves care away from "try this food and see" toward "this specific bacteria is missing, let’s replace it". Health beyond the gut (skin, mood, and weight) What’s changed: The study highlighted how these new bacteria produce metabolites that regulate inflammation and the immune system. What it means for you: Improving your dog's gut health may soon be a primary treatment for non-digestive issues, like allergies , anxiety , and obesity . Personalised nutrition becomes more important What’s changed: The discovery of a "core" microbiome of 240 species gives a gold standard for what a "healthy pet" looks like, and shows that a personalised approach may be needed per pet. What it means for you: In the near future, pet food companies may offer diets tailored to your dog’s specific microbiome profile, making sure they get the exact fibres needed to feed their unique "good" bacteria. How to support our tailmate’s gut health So, what we put in our pets’ bowls can have a big impact on their microbiome and, by extension, your pet’s health. That means, as well as making sure our pets’ diet is nutritionally balanced, we also need to make sure we keep a few things in mind when feeding them. A well-balanced diet Our pets get a good balance of macronutrients, with a focus on fibre and protein. We have an in-depth guide on pet nutrition that can help guide you here. In terms of what food to pick, we recommend always choosing a reputable brand that has been formulated with the help of a veterinary nutritionist. This ensures that the food has been correctly balanced for your pet’s needs. Your chosen diet should feature a named animal protein towards the top of its ingredients list and should be suitable for your dog’s age and size. Most vets don’t recommend raw feeding at this time due to the proven health and safety risks involved. But there are a whole array of good quality kibble, wet food, or even pre-prepared fresh cooked diets out there to choose from. Don’t switch food quickly Don’t switch foods quickly or overnight. We’ve all been there: we make a switch, and there’s a big mess to clean up. We need to do things gradually so our pet’s microbiome can “catch up”. Studies show microbial communities can shift and stabilise within six days of a diet change but gradual changes are still best. You should mix your pet’s old food in with the new food for at least a week, slowly changing the proportions. Research on puppies found that gradual dietary changes increased beneficial bacteria while reducing diarrhoea rates. But abrupt changes? They decreased beneficial Turicibacter and Lactobacillus while increasing potentially harmful bacteria. That’s not good news! Use a mix of prebiotics, probiotics and postbiotics Making sure that your pet has the right mix of prebiotics, probiotics and postbiotics can support their digestive system. Here’s what each of these are: If your pet is having problems with their digestion, your vet may recommend a mix of these to work together to support your pet’s microbiome. Warning signs that something's off with your pet's gut Ways to get those gut bacteria back on track First of all, it's important to get a diagnosis from a vet. Some of the symptoms on the above list can be associated with medical conditions like pancreatitis . If other illnesses have been ruled out, then you could support your pet’s digestive health by: What's actually hurting your pet's microbiome When should you consider microbiome testing? Microbiome testing might sound like something from the future, but private companies are now offering microbiome testing for pets. Healthy adult pets may benefit from microbiome testing as part of their preventive care. Think of it as a wellness check for the trillions of little guys keeping your pet’s gut ticking. Pets with diagnosed tummy issues may need frequent testing, and vets can use this information to track how treatment is going or to diagnose complications. Always speak to your vet if you have any questions about your pet’s digestive health.

Pet microbiomes and gut health, explained

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