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 Bec, August 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 Magazine, Australian 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: www.drbecvet.com and she may be contacted at bec@drbecvet.com
References:
[1] Similarity of the dog and human gut microbiomes in gene content and response to diet - Microbiome. 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 - https://pubmed.ncbi.nlm.nih.gov/27641441/
[3] Gut Microbiota in Anxiety and Depression: Unveiling the Relationships and Management Options - Pharmaceuticals (Basel). 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. - https://pubmed.ncbi.nlm.nih.gov/34509665/
[5] Characterization of microbial dysbiosis and metabolomic changes in dogs with acute diarrhea - PLoS One . 2015 May 22;10(5):e0127259. https://pubmed.ncbi.nlm.nih.gov/26000959/
[6] Factors Affecting Gut Microbiota of Puppies from Birth to Weaning - Published online 2023 Feb 6. doi: 10.3390/ani13040578