Keeping your dog’s microbiome healthy

By Dr. Vicky Simon


‘One of the most interesting developments in human medicine has been an increased understanding of the role that the gut microbiome (aka gut flora, being the microorganisms, including bacteria, archaea, fungi, and viruses, which live in our digestive tracts) has to play in both our physical and mental health. Now, scientists are starting to turn their attention to the canine gut microbiome. Dr Vicky Simon offers some practical tips on how to ensure that your dog’s microbiome is healthy!’

A healthy microbiome is one which contains a great diversity within its populations of microbes. What you or your pets eat, what they come into contact with and what medications they take can hugely influence it. The microbiome is so complex and variable throughout the body, and to such a degree that each surface of each tooth can have a slightly different microbiome!

Diet obviously plays a huge role in keeping your microbiome healthy. Some foods are considered ‘alive’, whilst others are considered ‘dead’. Generally, any highly heated or processed food is considered ‘dead’ as far as your microbiome is concerned. It gives them nothing that excites them or helps them to flourish. Raw foods are very ‘alive’ as they have their own microbiome, which can add diversity to the microbiome they join when eaten. This is one reason why a raw food diet is so great for dog and cats, and why it’s so important that horses, small furries and ruminants also get lots of fresh foods in their diet. Too much sugar and too many processed foods can encourage more pathogenic microbes to flourish, whereas a fresh whole food diet encourages more healthy microbes.

Another way diet can help the microbiome is through prebiotics. These are foods that contain high levels of insoluble fibre, that doesn’t get digested like soluble fibre, but feeds the bacteria in the colon. These are an essential inclusion for health, as there are some nutritional substances that we only get if the bacteria in our colon produce them and they can only do that if we give them insoluble fibre. For example, short chain fatty acids, such as butyrate, propionate and acetate. Great prebiotic foods include dandelion root, psyllium husk, marshmallow root, slippery elm bark, and many others. These foods are also great additions if your dog suffers from chronic anal gland issues.

Fermented foods are becoming huge in the human health industry, and they are creeping into the veterinary world too. There is a plethora of pet probiotics available, but many of them only contain one strain of bacteria, maybe 2 or 3 in others. Some human probiotics are like this too, although others contain many more strains. If you just take, or give to your pet, the same probiotic all the time then you are just adding one or a few strains. This is really only useful if you are lacking in this strain, so although it may help short term, longer term you need to get some variety in.

This is why I LOVE fermented foods – each different food that is fermented, creates a different selection of microbes during its fermentation. There is also some variety in the populations depending on the fermentation process. So, by feeding a selection of fermented foods you are adding a plethora of different microbes to your own or your pet’s microbiome. It’s also fun because these are foods that you can share with your pet to improve the health of you both.

Examples include Sauerkraut (cabbage, although other veg can be mixed in with it), Kefir (milk, coconut milk or coconut water), Yoghurt (dairy or non-dairy milks), Kimchi (Chinese leaves and/or other veg, usually with onion/garlic and chilli but avoid these in pets), etc. The possibilities are endless as most vegetables can ferment. If you want to try fermenting at home then I would recommend you find a good resource, like a book or website, to guide you until you know what you’re doing. In America they have a pioneering pet food company called Answers, who make fermented raw pet food, could this be the future of pet food?

If fermenting seems a bit out of your comfort zone, then probiotics can be given, but I always advise to rotate between different products if using them long term, to ensure you are benefitting the microbiome, by adding the diversity it needs. You might be able to switch between a couple of different pet probiotics, and I often rotate in human ones too. Just get in the habit of checking what strains are present so you aren’t giving the same strain in different forms!

Finally, medications can have a huge influence on the microbiome, especially antibiotics. These are indiscriminate in the body, killing both good and bad bacteria, so although they can help resolve infections with pathogenic bacteria, they can also knock down a lot of the great and healthy populations throughout the body, but especially in the gut. For this reason, it is so important to use antibiotics responsibly, and where needed only, rather than as preventatives or ‘just in case’. It is also important to select the correct antibiotic, and this is where the more modern culture of swabbing to test for sensitivity and resistance is great progress. Antibiotics save lives, there is no doubt about that, but we are depending on them far too much, and they are frequently given unnecessarily. As pet owners, as well as for us as vets, we should always be questioning if they are needed or not, every single time it is considered. Remember, you can always call back the next day or the day after, having not taken any antibiotics away to ask for some, but once you start a course you have to complete it to prevent antimicrobial resistance developing.

Also consider that what you put on your own, or your pets skin affects the microbiome there. This means that even topical antibiotic or antimicrobial treatments can change the long-term health of the affected area. However, they have a lesser impact than systemic antibiotics, which spread all over the body in the bloodstream and can affect the microbiome in many locations at once. Due to the rapid absorption of products through the skin, many advocators of natural health say that ‘if you wouldn’t put it in your mouth, don’t put it on your skin’. This totally makes sense, even more so with pets than humans, as they are prone to licking off whatever you might apply onto their skin anyway! Recently, in the next step forwards in the use of probiotics, there are many topical probiotic treatments being produced. These have been specialised for use on the skin, in the ears, in the mouth, in wounds, and even as cleaning products, where they out-compete with bad bacteria over time to create a more balanced and healthier microbiome in the affected area. I have recently started using some in my practice and I just love the ‘pro-life’ idea behind them. Disinfectants target all bacteria, but wouldn’t it be better to encourage the growth of all the good bacteria, whether in the ear canal, in the mouth or on the floor?!

Herbal medicines can influence the microbiome too. Immuno-modulating herbs can encourage the body’s own immune system to regulate its microbiome, whilst microbial modulators can directly influence the microbial populations. Either way there is discouragement of unhealthy populations of pathogenic microbes and encouragement of healthy populations of non-pathogenic microbes. This is where there is a fine line between what is diet and what is medicine, but as a herbalist it is a line I dance on both sides of with my patients. Any pet that is prone to recurrent infections, chronic low-grade infections, or wounds that aren’t healing, might benefit from some herbal assistance, for both immune support, but also for helping to rebalance that microbiome, especially if they have had lots of antibiotics.

If you are interested in the microbiome then Missing Microbes by Martin Blaser is a fascinating read. Super geeky, but super interesting!

Dr. Vicky Simon BVetMed VetMFHom MRCVS is based in Taunton, Somerset. Her website is You can email her or call her on 01984 624999.

Two other sources of useful information on the canine microbiome subject are below:,perfringens.