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Tummy to Temperament: How Canine Gut Health Affects Behaviour

The canine ‘gut microbiome’ refers to the incredibly diverse community of bacteria, fungi, viruses, and other microbes or microorganisms that live in a dog's gastrointestinal (GI) tract, or gut. And it’s not just about bacteria; it turns out many viruses are essential to health too.

But firstly; the gut comprises the entire intestinal tract, beginning in a dog’s mouth, and ending at their anus. And it turns out, the gut is responsible for innumerable functions, not simply digesting food. Research shows the canine gut microbiome is very closely related to ours [1] and we also share microbes with our companions. Sharing our homes with dogs (and cats) is great for pet parents’ microbiome health, too.

These microscopic critters have co-evolved with our dogs, helping to optimise food digestion, regulate the immune system, mood, and even produce essential vitamins, such as B vitamins and vitamin K.

The Emerging Science of the Gut-Brain Axis

That feeling of ‘butterflies in your stomach’ when you’re nervous? Feeling ‘sick to your stomach’ when you hear bad news? Having a ‘gut feeling’ about something? All of this, in humans, is now being attributed to a very real connection [2] between our microbiome and brain. The gut microbiome influences the development of the brain and are now implicated, in humans, in numerous neurological diseases, including dementia, and conditions such as depression, anxiety, autism, and bipolar disorder. [3]

The same goes for our dogs.

The interaction between the microbiome and the brain is facilitated several ways, involving neural connections via the vagus nerve, immune system pathways, and specific chemicals produced by gut bacteria, called metabolites.

Let’s define the canine microbiome in greater detail.

Composition of the Canine Microbiome

Dogs harbour distinct microbiomes throughout their body, varying with location, e.g.: ear canal, skin, respiratory tract, urinary tract, and gut, etc. Most studies in dogs have centred the gut microbiome, though it’s critical to keep in mind that other microbiome populations throughout the body have impacts on health. [4]

The composition of the canine microbiome varies according to a dog's genetics, sex, age and diet, environment, medications, and general health.

When present in a harmonious balance, healthy microbes promote wellbeing, though when the microbiome is out of kilter, this is called ‘dysbiosis.’ Dysbiosis is associated with numerous canine diseases, ranging from intestinal disorders, skin issues, obesity, arthritis, and behavioural problems.

That said there is a little bit of a ‘chicken and egg’ element here: is the microbiome unbalanced before the disease begins, or does the disease cause dysbiosis? Or is it a bit of both?

In Texas, veterinarians and scientists test dog stool samples for this imbalance, using the ‘dysbiosis index’.

Unfortunately, this test is not available in Australia, but the Texas group have identified bacteria that are present in high levels in healthy dogs, and not in unwell dogs. [5]

At birth, and as puppies, dogs acquire their microbiome from their mothers, however its structure and composition changes throughout life. [6]

The microbiome has fundamental roles in:

#1. Digestion and Nutrient Absorption

Microbes break down dietary fibres, resistant starch and proteins that are otherwise indigestible for dogs. This process produces compounds, called short-chain fatty acids (SCFAs) that nourish the gut cells, maintaining the health and integrity of the intestinal lining. 

These SCFAs are also neuroprotective, promoting brain health.

#2. Regulation of the Immune System

The microbiome trains the immune system to recognise pathogens, whilst ignoring healthy microbes, harmless substances, and the body’s own cells. The microbiome prevents allergies and autoimmune diseases developing. An abnormal immune response towards healthy gut bacteria is implicated in inflammatory bowel disease. [7]

Dogs with this condition typically have microbiome dysbiosis and faecal microbial transplants (FMT), where faeces from healthy dogs is transplanted into the intestines of dogs with chronic gut disease, is becoming a routine, effective treatment. (In fact, FMT is being explored in clinical trials for a myriad of human illnesses).

In dogs, FMTs use non-obese donors, as amazingly, faeces from obese dogs causes obesity in recipients.

#3. Integrity of the Gut Barrier

The lining of the gut acts as a barrier between foreign materials (such as toxins, bacteria, food allergens etc.) and the blood. During digestion, beginning in the mouth and ending with the excretion of waste products, as faeces, only certain substances should be absorbed by the intestines.

A balanced microbiome maintains the integrity of this barrier, the so-called gut mucosal barrier. 

Disruption of this barrier, by certain compounds, pathogens, and an abnormal microbiome increases the permeability of the gut lining. This is sometimes referred to as ‘leaky gut syndrome’. Increased permeability allows harmful substances and microbes direct access the blood stream, causing widespread inflammation and numerous disease conditions.

#4. Production of Neurotransmitters

Some of the microbes in the gut produce neurotransmitters, the chemical messengers regulating mood, behaviour, appetite, and sleep. More than 90% of the body’s ‘happy’ neurotransmitter, serotonin, is produced in the gut. Certain types of gut bacteria produce γ-aminobutyric acid, or ‘GABA,’  which has a calming impact on the brain. Other neurotransmitters, involved in the ‘fight or flight’ response, and other body functions are also produced in significant quantities by the microbiome.

The microbiome has a significant impact on a dog’s memory and ability to learn as they age. 

Certain canine phobias and aggressive behaviour have been linked to high levels of particular bacteria, and modulation of the microbiome is being investigated as a treatment modality in behavioural disorders. Research has identified microbiome associations in canine epilepsy and auto-immune disorders affecting the canine brain.

#5. Vagal Nerve Communication

The vagus nerve is the major ‘super-highway’ between the gut and the brain. Some gut bacteria stimulate this nerve directly, sending signals to the brain. This pathway plays a role in regulating stress responses and significantly impacting a dog's behaviour.

#6. Detoxification

The gut microbiome is critical in detoxifying various harmful ingested compounds. I suspect Hilda, my carrion-loving Irish Wolfhound has a particularly excellent microbiome, in this respect.

Detoxification protects dogs against acute toxicity, whilst preventing accumulate of compounds to toxic levels.

The microbiome impacts the way the body metabolises drugs. This may explain why some dogs with the same disease respond to certain treatments whilst others do not. In humans with cancer, the microbiome is determining the response to immunotherapies. The same likely applies to our dogs and pet dogs with cancer are in clinical trials investigating this.

#7. Competition with Pathogens

A healthy, diverse microbiome may prevent colonisation with harmful bacteria, by competing for nutrients and attachment sites along the gut lining. This ‘competitive exclusion’ guards against gut infections and overgrowth of harmful bacteria, causing dysbiosis.

Dysbiosis may increase production of certain toxins or metabolites, affecting brain function and behaviour. Research shows [4] that overproduction of ammonia and certain bacterial metabolites, contributes to cognitive decline and erratic behaviours in dogs.

What can I do to improve my dog’s microbiome?

To understand how we can improve our friend’s microbiome, we need to understand the modifiable factors contributing to dysbiosis. The most common culprits are antibiotics, dietary changes, and periods of illness or stress.

The primary way we can impact the gut microbiome is through feeding a diet supporting good microbes and intestinal health, and adding healthy microbes to the gut, via food.

✔️ A Balanced, Diverse Diet

Dog food is a controversial, impassioned topic, but there are some non-negotiables when it comes to the microbiome.

Feed a high-quality diet that meets the AAFCO's (Association of American Feed Control Officials) standards and is appropriate for your dog's size, life stage and health status. You can supplement this with various proteins and vegetables, providing a plethora of beneficial nutrients, microbes, and environmental enrichment for your pup!

Incorporate fresh, unprocessed foods that are safe for dogs. Bone broth, without seasonings and additives, is rich in gelatine and other nutrients, supporting the gut lining and is also anti-inflammatory.

Greek yoghurt (in dairy-tolerant dogs) is another good addition, providing beneficial live bacteria. Clean fresh water is essential. Dirty bowls with biofilms [8] and mould contribute to dysbiosis.

I recommend pet parents research diet, visiting evidence-based sites

If you plan to make food at home, please work with a veterinarian and nutritionist to ensure a balanced diet.

Vet confession: I struggle to balance my own diet, let alone make a complete diet at home for Hilda, so I supplement kibble with whole foods.

✔️ Consider Probiotics and Prebiotics

  • Probiotics are beneficial bacteria, added to the diet, which can temporarily help balance the microbiome.

Probiotic labels should include:

  • the exact probiotic species (e.g., Bifidobacterium longum).
  • the number of microorganisms (probiotics are measured in colony forming units, or CFU; 1-10 billion CFUs daily are recommended for dogs).
  • an expiry date and storage conditions; and
  • a guarantee for the number of live organisms. 

The manufacturer should provide research to support claims, and probiotics should be externally audited and accredited. There is a vast difference in quality between brands, and I recommend you discuss choice with your veterinarian.

  • Prebiotics are non-digestible fibre that serves as food for the beneficial bacteria. [9] Prebiotics may include beet pulp, chicory root, gum arabica and high fibre vegetables.

(Synbiotics = a probiotic and prebiotic administered together).

✔️ Avoid Unnecessary Antibiotics

Antibiotics save lives and are essential for treating certain bacterial infections. However, they damage the microbiome, and must be used judiciously, and only under veterinary guidance. Inappropriate use also creates antibiotic resistance, affecting our pets and us.

✔️ Regular Worming

Routine worming protects against intestinal parasites (worms), which may damage the gut lining, promoting dysbiosis. Parasites can also be zoonotic, infecting humans.

✔️ Exercise

Regular exercise creates a more diverse and balanced gut microbiome for your pup and for you! Grab that leash.

✔️ Minimise Stress

Chronic stress alters the microbiome, affecting digestion. Reduce stress in your dog’s environment with a comfortable living space, and importantly, a consistent routine. Positive training methods, socialisation, and environmental enrichment are also critical.

✔️ Limit Exposure to Toxins

Pesticides, herbicides, and cleaning agents negatively affect the gut health [10]. Ensure your dog's environment is free from these harmful agents where possible.

✔️ Regular Vet Visits

Check in with your vet to detect any health issues early. At minimum, an annual check-up is recommended.

✔️ Finally, avoid sudden changes in diet or introduction of supplements, and reach out to your vet when in doubt. Note any changes in your dog's stool, weight, thirst, appetite, energy levels and behaviour, as all of these may reflect changes in gut health and other diseases.

The canine microbiome has enormous influences on physical and mental health, and by appreciating this we can really help our friends. As the science progresses, more intervention and treatments will become available, so watch this space!

written by Dr BecAugust 2023 for Australian Dog Lover (all rights reserved).

About our writer

Dr Bec is a Melbourne-based veterinarian and academic, working in the clinic, animal welfare, the media and medical research. She has a passion for sharing fascinating facts and the latest research on the intriguing lives and science of all animals, particularly those we share our lives with.

Dr Bec is a regular guest on Melbourne radio, a columnist for Australian Dog Lover MagazineAustralian Cat Lover Magazine, and Pet Insurance Australia, and she presents short segments on all things animal related (see Insta and Facebook). Her emphasis is on sharing of evidence-based veterinary advances and the empowerment of pet parents, and society, through promoting medical literacy, or the understanding of our pets’ health, and our own. She relishes reaching out to all animal loving audiences.

Her academic and clinical research spans several areas, with a focus on the role of the microbiome in pet health, preventative medicine, developing new veterinary medicines, clinical trials that benefit animals and humans, and working to prevent antibiotic resistance.

Dr Bec advocates for animal charities that promote animal welfare, in Australia and overseas.
Her blog can be found at: and she may be contacted at


[1] Similarity of the dog and human gut microbiomes in gene content and response to diet -  2018; 6: 72. Published online 2018 Apr 19. doi: 10.1186/s40168-018-0450-3

[2] Gut instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration

[3] Gut Microbiota in Anxiety and Depression: Unveiling the Relationships and Management Options -  2023 Apr; 16(4): 565. Published online 2023 Apr 9. doi: 10.3390/ph16040565

[4] Dogs' Microbiome From Tip to Toe, Published online Epub 2021 Sep 10. -

[5] Characterization of microbial dysbiosis and metabolomic changes in dogs with acute diarrhea - PLoS One . 2015 May 22;10(5):e0127259.

[6] Factors Affecting Gut Microbiota of Puppies from Birth to Weaning - Published online 2023 Feb 6. doi: 10.3390/ani13040578 

[7] Humoral immune responses against gut bacteria in dogs with inflammatory bowel disease - PLoS One - 2019 Aug 1;14(8):e0220522.

[8] It's a Long Way to the Tap: Microbiome and DNA-Based Omics at the Core of Drinking Water Quality - Int J Environ Res Public Health. 2022 Jun 28;19(13):7940.

[9] Role of Gut Microbiota, Probiotics and Prebiotics in the Cardiovascular Diseases 2021 Feb; 26(4): 1172. Published online 2021 Feb 22. doi: 10.3390/molecules26041172

[10] Gut microbiota: a non-target victim of pesticide-induced toxicity  2023; 15(1): 2187578. Published online 2023 Mar 15. doi: 10.1080/19490976.2023.2187578

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