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What Happens When Dogs Eat More Fibre? New Science Reveals Gut Secrets

Fibre – it’s not just for humans. While we often hear about its benefits for our own digestive health, what about our dogs? A fascinating new study by Bhosle et al. (2025) reveals how increasing dietary fibre affects the trillions of microbes living in a dog’s gut – and the important compounds they produce.

June 16, 2025 • 3 min read

Bushra Schuitemaker

Lead Microbiologist

At BIOME9, we use our GutDiscovery® microbiome testing kit to uncover what’s really happening inside the guts of dogs with digestive issues and other health concerns. Naturally, I was curious to see how a fibre-rich diet would affect the microbiome and metabolome (the small molecules made by microbes) in healthy dogs. And what we saw echoed much of what we’re finding in our own database.

Did you know that over 90% of the dogs we’ve tested have poor fibre digestion scores (below 50 [FIGURE 1])? This means their microbiomes are not well equipped to break down fibre. And that matters, because it’s the gut bacteria - not the dog’s body - that digest fibre. When they do, they produce powerful compounds like short-chain fatty acids (SCFAs), which have wide-ranging benefits across the body.

FIGURE 1: Histogram of 1,314 GutDiscovery® scores for Fibre Digestion collected between March 2024 and May 2025.

What is ‘Gut Fuel’ and why is it important?

In our GutDiscovery® reports, we include a score called Gut Fuel [FIGURE 2], which reflects the bacteria capable of producing SCFAs. We consistently see a positive correlation between fibre digestion and SCFA production, so when one is low, so is the other [FIGURE 3].

FIGURE 2: Example of Gut Fuel score in Part 2 of the GutDiscovery® report.

These SCFAs help modulate the microbiome, reduce inflammation, support gut barrier function, and even allow bacteria to directly “talk” to gut cells. In short, fibre is the food, but Gut Fuel is the fire that powers microbial health.

FIGURE 3: Scatter graph of Gut Fuel (Y-axis) and Fibre Digestion (X-axis) from 1,314 GutDiscovery® scores collected between March 2024 and May 2025.

The study in a nutshell

Twelve healthy adult dogs were fed a typical commercial diet, then switched to a high-fibre version of the same diet. The researchers collected faecal samples and analysed both the microbial composition (using shotgun metagenomic sequencing) and the metabolites (using mass spectrometry).

Why is this important? Because the gut microbiome doesn’t just help digest food, it also produces chemicals that can affect inflammation, gut health, and even brain function e.g. the function of the microbiome - not just WHO is in there, but WHAT do they do? Understanding how diet affects these microbial communities and their activity provides a powerful tool for supporting canine health.

So what changed?

After just 5 weeks on the high-fibre diet, the dogs’ gut microbes had already shifted in noticeable ways:

A boost in “good” bacteria: There was an increase in Bifidobacteria and Faecalibacteria, microbes linked with anti-inflammatory effects and better gut health in both humans and dogs.
A decrease in potential troublemakers: Levels of Clostridium sensu stricto 1 and Escherichia-Shigella went down. These can sometimes contribute to inflammation or dysbiosis (a microbial imbalance), particularly when they become overgrown.
Significant shifts in microbial activity: The dogs’ metabolomes changed too, especially in molecules linked to protein and carbohydrate breakdown. This shows that fibre isn’t just feeding the dog, it’s feeding their gut microbes, which then produce different compounds.

What does this mean for your dog?

Not all fibre is created equal, but adding the right kinds of fibre can encourage a healthier gut environment. This study reinforces what we see at BIOME9: dietary fibre can help nurture beneficial microbes, reduce the abundance of less helpful ones, and shift the gut ecosystem in a positive direction.

However, the study results varied significantly between the dogs; i.e., for some dogs, changing their diet alone is sufficient for modulating the microbiome, while others may require additional support, such as supplements. It came down to the initial baseline of the microbiome, so you need to test your dog's gut to know what will work. Additionally, this is why some dogs show improvements quickly, while others take longer.

It’s not about feeding your dog huge amounts of fibre overnight. The key is balance and quality, and every dog is different. That’s where our GutDiscovery® test can help. By understanding what’s going on inside your dog’s gut, we can work with vets and nutritionists to make evidence-based recommendations tailored to each dog.

Take-home message

Fibre matters, not just for digestion, but for shaping a healthier microbiome. And the microbiome, in turn, plays a key role in your dog’s overall health.

This study gives us yet more evidence that what we feed our dogs can powerfully affect their inner ecosystem. At BIOME9, we’re excited to keep learning, and to turn this knowledge into better outcomes for dogs everywhere.

Frequently asked questions

The microbiome is the name given to the collection of microbes, mostly bacteria, but also fungi and protozoa, that exist within your dog’s gut. It is a diverse and complex microbial community which can directly affect health and wellbeing. We know that 90% of a human’s body cells are microbes, with only 10% being human cells – it’s just that human cells are markedly larger than the microbes. It’s similar for our four-legged friends. Testing the microbiome gives us an idea of exactly which bacteria are present in your dog’s gut and this can help indicate existing or future health problems.
A healthy diversity within the microbiome has been found to be an accurate indicator of overall health and wellbeing. If your dog appears healthy, but has an imbalance in their microbiome, then this could be an indicator of a potential future health issue. If your dog has any existing health complaints, then improving the health of their microbiome can help to improve immune system health and overall wellbeing, as well as improving disease symptoms.
Testing and treatment have the potential to help with a whole range of different health complaints. The immune system is very closely associated with the gut, so any imbalance in the microbiome can influence immune system health, overall vitality and wellbeing. Our supplement recommendations are also tailored to your individual dog, with specific ranges designed to help with gastrointestinal inflammation, joint problems, allergies and skin complaints, to name a few.
All you need to do is order a kit online and fill in our questionnaire about your dog and their general health. We will then send the kit out to you by post. You then just need to collect a sample and return it to us, again by post. Once the test is performed, we will email the results directly to you.
You do not need to get your vet’s permission to test, or talk to them about performing the test beforehand. We do recommend that you pass on a copy of your test results to your regular vets, as it may help them in understanding your pet’s current health, and any future complaints they may have.