The dog gut microbiome explained (by a vet)
We’ve been posting a lot about the dog gut microbiome, but what exactly is it? In this article, Dr Joanna Woodnutt MRCVS explains what your dog’s gut microbiome is, and what vets and scientists know so far about how it works. Stay tuned though – this is a rapidly evolving area of science!
What is the dog gut microbiome?
Inside your dog’s gut there’s a whole ecosystem. Millions of bacteria, yeasts and fungi live there. But this isn’t a bad thing – it’s entirely normal, and every animal has the same. This ecosystem is the dog gut microbiome.
What we as vets and medical professionals know is that the gut microbiome is an important part of your dog’s health. Far from being problematic, this ecosystem helps your dog stay healthy in ways we never could have anticipated.
What lives in the dog microbiome?
A healthy dog’s microbiome contains about 40 billion bacteria, split into over 150 genera and over 1500 species. The most abundant genera are Blautia, Peptacetobacter, Mediterranebacter, Faecalimonas, Clostridium and Fusobacterium. The healthier your dog’s gut, the more bacteria species they have in their microbiome. Alongside the bacteria, there are fungi (you might be familiar with Candida species, which make up most of the ~40 species living in your dog’s gut), viruses, and even nematodes – think like intestinal worms, but a non-parasitic version. These species live harmoniously and mostly digest things we can’t, like fibre.
How do they get there?
Your dog’s gut is populated by a starting population of bacteria from their mum at birth, especially when the birth is natural. They also pick up a few more here and there in early life, for instance when suckling. Your dog’s environment and diet will then impact what’s there – certain diets promote a more diverse ‘flora’, while antibiotics can kill off some bacteria, negatively impacting the diversity of the gut microbiome.
What do they do?
So, why is it so important to have a wide range of species in the gut? Well, that comes down to what the microbiome is for.
The species in our microbiome can digest things your dog can’t – like fibre, or nutrients that have made it past the small intestine – and in return for their meal, they allow your dog to absorb some of the by-products of their digestion. These by-products are nutrients your dog couldn’t make on our own. For example, your dog has tryptophan in their daily diet. While your dog will digest and use this itself, the bacteria in your dog’s gut can convert anything spare into anti-inflammatory metabolites that are important for immunity in the gut. We know now that if the right bacteria aren’t there to make these metabolites, or your dog isn’t getting enough tryptophan, this can cause symptoms of IBD.
In other words, we co-evolved to work together with our microbiomes. Your dog gives them a home in the gut and a ready supply of nutrients, and in return your dog’s microbiome produces nutrients your dog couldn’t get otherwise.
What is canine dysbiosis?
Canine dysbiosis is when the microbiome gets out-of-whack. A healthy microbiome has all those 1500 species of bacteria in balanced proportions, and even those that aren’t there in huge abundance have an important role to play. But in dysbiosis, some bacteria go crazy and overgrow, out-competing the less abundant species. Your dog’s gut goes from a balanced place with thousands of species, to the top 25 species dominating. By losing diversity, they lose some of the important functions of the dog microbiome.
This can happen due to stress, antibiotics, immune-mediated disease, bad diets, illness, and a whole host of other problems.
What causes bad bacteria in a dog’s gut?
It’s important to understand that the bacteria in dysbiosis aren’t necessarily bad bacteria. They’re all bacteria that should have been there anyway. The problem is the proportions that they’re in. If antibiotics kill off 10% of what’s in your dog’s gut, the fastest ones to return are those that are most abundant, and the balance is off. Or, if your dog is feeling really stressed and the cortisol and other hormones negatively impact some of the bacteria, the others will grow to fill their space – and the balance is off.
How do I know if my dog’s gut microbiome is out of balance?
If your dog’s gut microbiome is out of balance, there will usually be signs. These could be sudden in onset – like diarrhoea – or ongoing, like skin complaints. Signs your dog’s microbiome is unbalanced include:
- Diarrhoea (which can be sudden and severe, or intermittent and mild IBS-like symptoms)
- Vomiting
- Decreased appetite
- Rumbling gut (‘borborygmi’)
- Weight loss
- Increased susceptibility to disease
- Itching
- Poor skin or coat
- Obesity
- Anxiety
However, there are sometimes no signs of intestinal dysbiosis. For example, we know antibiotics cause dysbiosis, but not every dog on antibiotics will get symptoms of a problem.
How to test a dog’s gut microbiome
If you aren’t sure if your dog’s gut microbiome is out of balance or whether they’d benefit from microbiome support (such as dog probiotics, or a mix of prebiotics and probiotics), you can also test your dog’s microbiome. The test is very simple to use – you collect a fresh sample of your dog’s poo and send it off to a lab, where they use DNA testing to identify the bacteria that are present.
Find out more about dog microbiome testing (and get a discount!).
How to fix a dog gut microbiome
If you think your dog has signs of an out-of-balance microbiome or your dog microbiome test has come back saying they have dysbiosis, you’ll want help re-balancing your dog’s gut bacteria. To do this, you’ll need a combination of the best probiotics for dogs, and increased fibre and other dog prebiotics to help the gut microbiome thrive. If you’ve taken one of the dog microbiome tests we recommend, you’ll get an individual report to help you work out which fibres are best. If not, our article on dog prebiotics might help! Another option, especially where their symptoms are serious, is faecal microbiota transplantation – essentially giving them a ‘poo transplant’ from a healthy animal. This is something your vet can help you with, if you decide to go down this route.
Conclusion
Your dog’s gut microbiome is an ecosystem of other species living inside your dog, and it’s really important for their overall health. When the dog microbiome gets disrupted by stress, disease, or antibiotics, some bacteria over-grow, throwing off the balance – termed ‘dysbiosis’. Dog microbiome tests can be helpful so you can see what’s happening and make a plan for treatment, but you can also go ahead and start the best dog probiotics to support your dog’s recovery.
- The dog gut microbiome explained (by a vet) - March 10, 2025
- Dog Microbiome Tests (A Vet Explains) - March 5, 2025
- Prebiotics, Probiotics, and Postbiotics – What’s the difference? - February 28, 2025
