At BIOME9, our mission has always been to push the boundaries of canine gut health research and deliver the best microbiome testing and veterinary support.
Today, we’re excited to announce a new chapter in that journey: a collaboration with Pooch & Mutt.
This fresh new approach will continue to bring accessible, reliable, microbiome testing - paired with the same great supplements and expert advice you trust.
Insights from the BIOME9 Quarterly Industry Journal Club (September 2025)
The BIOME9 Industry Journal Club turned its attention to one of the most compelling themes in microbiome science today: the crossover between the human and canine gut microbiome. For decades, research in human medicine has informed our understanding and management of the health of companion animals. But increasingly, the exchange is proving to be reciprocal. Not only can we apply human findings to dogs, but studies in dogs are also shedding light on human disease mechanisms and therapies. Shared research is leading to shared benefits, a true demonstration of One Health and One Medicine in action.
Dogs are uniquely suited to this role. They share our homes, diets, and daily environments, so their microbiomes are shaped by many of the same influences as ours. They naturally develop a range of conditions that also affect people, including inflammatory bowel disease, obesity, anxiety, epilepsy, and cancer. At the same time, they are practical research partners: repeated non-invasive faecal sampling is straightforward, and dietary intake can be carefully monitored in real-world settings. These characteristics make dogs an exceptional model for microbiome research, offering opportunities not only to advance human health but also to directly benefit dogs most in need of targeted interventions.
Companion Animal vs Human Gut Microbiome
Recent advances in shotgun metagenomics have enabled scientists to compare the canine and human gut microbiome in unprecedented detail. A landmark dataset included thousands of dog stools analysed alongside human, pig and mouse samples, providing species-level genome bins, metabolic pathways, and antimicrobial resistance (AMR) profiles.
The results were striking. More than 200 species-level bins were identified in both dogs and humans, including Prevotella copri, Ruminococcus gnavus, and Bacteroides vulgatus. These microbes play key roles in carbohydrate metabolism and the production of short-chain fatty acids, which help maintain gut barrier integrity and regulate immune function. Despite these similarities, single-nucleotide polymorphism analysis revealed that the strains remain host-specific, evolving independently in dogs and humans.
Perhaps the most important finding is that dogs show greater microbiome similarity to humans than mice or pigs do. This challenges long-held assumptions about translational models. While pigs may be genetically closer and rodents historically dominate research, it is dogs whose microbiome most closely mirrors ours in both taxonomy and function. This reinforces the value of canine research not as a substitute for human data, but as a partner in generating insights that are more predictive and clinically relevant.
Cohabitation and Shared Microbiota
Dogs and humans do not just live together; they also exchange microbes. Cohabitation studies reveal that families, including their dogs, share microbial taxa at multiple body sites, with the strongest effect seen in the skin microbiome. Remarkably, your skin is more similar to your own dog’s than to another person’s dog, emphasising that microbial exchange is household-specific rather than universal.
For the gut, these environmental dynamics have important consequences. In dogs, gut microbiota composition shifts rapidly after adoption, sometimes within just a week. This echoes findings in humans, where even a house move can reset the microbial signature of a new home to reflect that of its inhabitants. The household, in effect, seeds the microbial environment in which both people and dogs live.
These environmental interactions are particularly relevant in disease states. In dogs with acute haemorrhagic diarrhoea or chronic enteropathies, beneficial taxa such as Faecalibacterium and members of the Ruminococcaceae family are consistently depleted, while opportunistic bacteria, including Clostridium perfringens, expand. Increased abundance of Sutterella, a genus frequently observed in inflammatory bowel disease, further mirrors patterns seen in humans, highlighting shared features of gut dysbiosis across species. The consistent losxs of Faecalibacterium in both canine and human IBD supports its role as a robust biomarker of microbial imbalance and recovery.
Figure 1: Comparison of gut microbiota in healthy dogs and dogs diagnosed with IBD based on BIOME9 data collected between March 2024 and August 2025. Dogs with IBD exhibit a higher relative abundance of(A)Sutterellaand(B)Clostridiumcompared to healthy dogs. In contrast, they exhibit reduced (C) species richness and (D) alpha-diversity as measured by the Shannon Index. These patterns reflect gut dysbiosis similar to that observed in human IBD.
From a One Medicine perspective, cohabitation is not just a curiosity; it may actively shape disease risk and resilience. It helps explain why both dogs and humans sometimes develop gastrointestinal or behavioural conditions following environmental upheavals such as rehoming, moving house, or extended separation.
The Gut–Brain Axis
The gut microbiome’s influence extends beyond digestion into behaviour and mental health, a connection known as the gut-brain axis. In both humans and dogs, altered microbiota have been linked to anxiety, depression, and aggression.
In canine studies, anxiety correlates with reduced SCFA-producing genera such as Coprococcus and Faecalibacterium. Aggressive behaviour has been associated with shifts in Lactobacillus and Turicibacter, taxa implicated in neurotransmitter regulation. Parallel human studies involving thousands of participants show that depletion of Coprococcus and Dialister is linked to depression, independent of antidepressant use. Microbial metabolites such as GABA and dopamine derivatives further connect the gut microbiome to neurological signalling and quality of life.
These parallels suggest profound translational opportunities. If certain microbial profiles predispose dogs to anxiety or aggression, microbiome-guided nutritional or probiotic interventions could form part of behavioural therapy. Conversely, naturally occurring canine anxiety provides a model for testing interventions relevant to human mental health, such as psychobiotics or dietary fibre supplementation.
Antimicrobial Resistance and the Shared Resistome
Antimicrobial resistance (AMR) is a pressing global health challenge, and companion animals play a role that cannot be ignored. Dogs and humans share bacteria, and with them, resistance genes.
Studies show that pet dogs, particularly those frequently exposed to antibiotics for common conditions such as ear infections or gastrointestinal issues, carry higher antimicrobial resistance gene burdens than strays. Alarmingly, resistance genes to last-resort antibiotics such as colistin (mcr-1) have been detected in both dogs and their owners. In some households, identical extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains have been found in both species, evidence of direct microbial sharing.
For One Medicine, the lesson is clear: antimicrobial stewardship must not stop at the clinic door. Pets can act as reservoirs and amplifiers of resistance, and effective surveillance requires a harmonised approach across human and veterinary medicine.
Oncology and Therapy Response
Cancer is another area where dogs offer translational insight. Unlike rodents, which require artificial induction of tumours, dogs naturally develop cancers such as lymphoma, mammary tumours, and colorectal cancer within the same environments humans inhabit. This makes them invaluable models for comparative oncology.
Early studies show that chemotherapy alters the canine microbiome within just one week, increasing dysbiosis and shifting metabolite production. These changes align with findings in human oncology, where antibiotic use and dysbiosis are associated with reduced efficacy of immunotherapies, such as PD-1 checkpoint inhibitors. Importantly, certain microbes, such as Akkermansia muciniphila, Lactobacillus, and butyrate producers, are consistently associated with improved responses across both species.
This raises the possibility that microbiome profiling could predict therapy outcomes in advance, guiding the use of probiotics, dietary interventions, or metabolite modulation to improve survival and quality of life in both dogs and humans.
Limitations & Challenges
While advances in canine microbiome research have generated valuable insights, several limitations and challenges must be acknowledged to maintain scientific integrity. Small sample sizes, heterogeneity in study populations, uncontrolled diets, and variability in laboratory methods all reduce reproducibility and limit cross-study comparisons. Taxonomic profiling alone does not fully capture microbial function, and species-specific differences can constrain the direct translation of findings to humans. Addressing these challenges requires careful study design, standardisation of protocols, and integration of functional data, while recognising that no approach can fully eliminate uncertainty. These limitations also underscore the importance of collaboration across disciplines and species, fostering a shared expertise that enhances study design, interpretation, and the translational relevance of microbiome research.
Table 1: Summary of key challenges in canine and comparative microbiome research, their impact on study outcomes, and potential strategies to mitigate these limitations.
Challenge
Impact on Research
Possible Solutions
Sample size & controls
Small cohorts in primary studies, lack of controls reduce statistical power and reproducibility
Larger, well-controlled studies; meta-analyses to pool data
Standardisation of methods
Variability in DNA extraction, sequencing, and analysis limits cross-study comparisons
Design interventions safe for each species; consult veterinary toxicology data
Composition vs function
Taxonomic profiles alone do not reveal metabolic or signalling roles
Integrate functional sequencing (metagenomics, metabolomics); interpret cautiously due to limited animal databases
Translational limitations
Differences between species may prevent the direct application of findings
Focus on shared mechanisms, validate findings in both species, and consider physiological differences
Shared Research, Shared Benefit
The evidence discussed in this Journal Club highlights a clear reality: dogs and humans are microbiome partners. Whether in gut disease, behaviour, antimicrobial resistance, or cancer, we share microbes, functions, and disease pathways. This shared biology creates opportunities for interventions that benefit both species, from diet and probiotics to cancer therapies.
The crossover between the human and canine microbiome is more than a scientific curiosity; it is a practical avenue for accelerating translational medicine. By continuing to study dogs not only as patients but as partners, we embrace the principles of One Medicine, advancing science that serves both human and animal well-being.
References
Companion animal vs human gut (shotgun)
Coelho, L.P. et al. (2018). Similarity of the dog and human gut microbiomes in gene content and response to diet. Microbiome, 6, 72.
Deng, P. and Swanson, K.S., (2015). Companion Animals Symposium: Future aspects and perceptions of companion animal nutrition and sustainability. Journal of Animal Science, 93(3), pp.823-834.
Cohabitation and shared ASVs (16S)
Song, S.J. et al. (2013). Cohabiting family members share microbiota with one another and with their dogs. PNAS, 110(26), 10604–10609.
Coelho, L.P. et al. (2022). Dog and human microbiomes converge through cohabitation. Microbiome, 10, 87.
Lax, S., Smith, D.P., Hampton-Marcell, J., Owens, S.M., Handley, K.M., Scott, N.M., Gibbons, S.M., Larsen, P., Shogan, B.D., Weiss, S. and Metcalf, J.L., 2014. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science, 345(6200), pp.1048-1052.
Gut-brain axis
Pilla, R. and Suchodolski, J.S., 2020. The role of the canine gut microbiome and metabolome in health and gastrointestinal disease. Frontiers in veterinary science, 6, p.502799.
Pellowe, S.D., Zhang, A., Bignell, D.R., Peña-Castillo, L. and Walsh, C.J., 2025. Gut microbiota composition is related to anxiety and aggression scores in companion dogs. Scientific Reports, 15(1), p.24336..
Valles-Colomer, M. et al. (2019). The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology, 4, 623–632.
Patel, K.V., Hunt, A.B., Castillo-Fernandez, J., Abrams, C., King, T., Watson, P. and Amos, G.C., 2024. Impact of acute stress on the canine gut microbiota. Scientific Reports, 14(1), p.18897
AMR and the shared resistome
Monteiro, H.I., Silva, V., de Sousa, T., Calouro, R., Saraiva, S., Igrejas, G. and Poeta, P., 2025. Antimicrobial Resistance in European Companion Animals Practice: A One Health Approach. Animals, 15(12), p.1708.
Guardabassi, L., Schwarz, S. and Lloyd, D.H., 2004. Pet animals as reservoirs of antimicrobial-resistant bacteria. Journal of antimicrobial chemotherapy, 54(2), pp.321-332.
Zhou, N., Chen, W., Xia, L., Li, M., Ye, H., Lv, C., Chen, Y., Cheng, Z., Park, T.J., Ho, P.L. and Gao, X., 2024. Metagenomic insights into the resistome, mobilome, and virulome of dogs with diverse lifestyles. Animal Microbiome, 6(1), p.76.
Zhao, R., Hao, J., Yang, J., Tong, C., Xie, L., Xiao, D., Zeng, Z. and Xiong, W., 2022. The co‐occurrence of antibiotic resistance genes between dogs and their owners in families. IMeta, 1(2), p.e21.
Menezes, J., da Silva, J.M., Frosini, S.M., Loeffler, A., Weese, S., Perreten, V., Schwarz, S., da Gama, L.T., Amaral, A.J. and Pomba, C., 2022. mcr-1 colistin resistance gene sharing between Escherichia coli from cohabiting dogs and humans, Lisbon, Portugal, 2018 to 2020. Eurosurveillance, 27(44), p.2101144.
Oncology and therapy response
Wirbel, J., Pyl, P.T., Kartal, E., Zych, K., Kashani, A., Milanese, A., Fleck, J.S., Voigt, A.Y., Palleja, A., Ponnudurai, R. and Sunagawa, S., 2019. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nature medicine, 25(4), pp.679-689.
Rossi, T., Vergara, D., Fanini, F., Maffia, M., Bravaccini, S. and Pirini, F., 2020. Microbiota-derived metabolites in tumor progression and metastasis. International Journal of Molecular Sciences, 21(16), p.5786.
Gopalakrishnan, V., Spencer, C.N., Nezi, L., Reuben, A., Andrews, M.C., Karpinets, T.V., Prieto, P.A., Vicente, D., Hoffman, K., Wei, S.C. and Cogdill, A.P., 2018. Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Science, 359(6371), pp.97-103.
Aluai‐Cunha, C.S., Pinto, C.A., Correia, I.A.D.F.L., dos Reis Serra, C.A. and Santos, A.A.F., 2023. The animal's microbiome and cancer: A translational perspective. Veterinary and Comparative Oncology, 21(2), pp.166-183.
Santiago-Rodriguez, T.M., 2024. Comparative oncology using domesticated dogs and their microbiome. Frontiers in Veterinary Science, 11, p.1378551.
Kleber, K.T., Iranpur, K.R., Perry, L.M., Cruz, S.M., Razmara, A.M., Culp, W.T., Kent, M.S., Eisen, J.A., Rebhun, R.B. and Canter, R.J., 2022. Using the canine microbiome to bridge translation of cancer immunotherapy from pre-clinical murine models to human clinical trials. Frontiers in immunology, 13, p.983344.
Zheng, H.H., Du, C.T., Yu, C., Tang, X.Y., Huang, R.L., Zhang, Y.Z., Gao, W. and Xie, G.H., 2022. The relationship of tumor microbiome and oral bacteria and intestinal dysbiosis in canine mammary tumor. International Journal of Molecular Sciences, 23(18), p.10928.
We’re excited to announce that the Pooch & Mutt Gut Health Test is now live, bringing accessible, science-backed microbiome testing directly to dog owners. Powered by BIOME9’s technology and research, this new at-home offering supports personalised nutrition through reliable gut health insights, and targeted supplement plans.
While the Gut Health Test is designed for at-home use by pet parents, BIOME9’s GutDiscovery® test remains the gold standard for veterinary professionals and researchers - to access high-resolution data for clinical, behavioural, and nutritional applications.
Together, these two offerings work in harmony, ensuring that all dogs, from the couch to the clinic, can benefit from a better understanding of their gut microbiome.
BIOME9 GutDiscovery® vs. Pooch & Mutt Gut Health Test: Understanding the Differences for Veterinary Professionals
The canine gut microbiome is a complex ecosystem influencing health, immunity, digestion, and behaviour. As veterinary professionals, making informed decisions about diagnosis, treatment, and nutritional advice increasingly depends on accurate and detailed microbiome analysis.
At BIOME9, we’re proud to offer cutting-edge microbiome testing designed to meet the needs of professionals and large-scale research projects - while Pooch & Mutt provide accessible, consumer-focused testing to support general nutritional guidance, utilising the same science-backed supplement plans.
The Evolution of Microbiome Testing in Veterinary Practices
BIOME9’s GutDiscovery® test represents the forefront of microbiome science. It uses full-length 16S rRNA long-read sequencing (Oxford Nanopore platform) to deliver species-level resolution and detailed pathogen detection. This high taxonomic precision allows vets, nutritionists, and behaviourists to gain deeper insights into the microbial communities affecting a dog’s health, insights that are critical for making clinical, nutritional, and behavioural decisions that truly target underlying issues.
In contrast, Pooch & Mutt’s Gut Health Test, powered by BIOME9 technology, employs short-read 16S sequencing focusing on the V4 region (Illumina NovaSeq platform). This approach offers broader coverage and greater read counts, making it highly sensitive and effective for general profiling and dietary recommendations. While it provides genus-level resolution and validated health scores consistent with BIOME9 standards, it lacks the finer species-level detail necessary for complex clinical cases.
Why BIOME9 GutDiscovery® Is Essential for Professionals
Species-Level Identification and Pathogen Detection: GutDiscovery’s long-read sequencing enables precise differentiation between closely related bacterial species, including potentially pathogenic strains. This level of detail is essential when diagnosing dysbiosis, infections, or chronic gut conditions.
In-Depth Functional and Health Insights: Beyond taxonomy, GutDiscovery analyses microbial diversity, richness, balance, resilience, and provides comprehensive health indicators, including immune, digestive, and metabolic function scores, to inform personalised interventions.
Clinical and Nutritional Decision Support: The detailed microbiome profile helps vets and nutritionists tailor treatment plans, supplements, and dietary strategies that address specific microbial imbalances or deficiencies. This targeted approach can support management of inflammatory bowel disease, behavioural issues linked to the gut-brain axis, and other complex health challenges.
Insurance Recognition: Increasingly, pet insurers are covering GutDiscovery® tests when recommended by veterinary professionals, recognising its value in providing actionable insights that improve patient outcomes.
Pooch & Mutt Gut Health Test: A Great Tool for General Nutritional Guidance
Pooch & Mutt’s Gut Health Test is designed for ease of use and accessibility, making it ideal for pet owners seeking general gut health insights and nutritional recommendations. Its genus-level analysis delivers a reliable overview of the core microbiome, health scores, and recommended supplement plans, based on validated standards derived from BIOME9’s extensive database of over 1,400 dogs.
This approach works well for guiding dietary choices and routine supplementation, but doesn’t provide the species-level resolution or pathogen detection necessary for clinical diagnostics or detailed behavioural investigations.
Comparative Overview
Feature
BIOME9 GutDiscovery®
Pooch & Mutt Gut Health Check
Sequencing Platform
Oxford Nanopore (long-read)
Illumina NovaSeq (short-read)
16S rRNA Region
V1–V9 (full-length)
V4 (middle region)
Taxonomic Resolution
Species-level and above
Genus-level and above
Reads per Sample
20,000 – 40,000
100,000 – 200,000
Turnaround Time
~14 days
~4 weeks
Pathogen Analysis
Yes
No
Health Indicators
Immune, digestive, and metabolic function
Immune, digestive, and metabolic function
Clinical/Nutritional Use
In-depth complimentary diagnostics and nutritional advice
General nutrition and personalised supplement plans
Insurance Coverage
Increasingly accepted with vet recommendation
Not typically covered
Collaborative Advancement
At BIOME9, we’re committed to advancing veterinary microbiome science through professional services, bespoke health plans, and large-scale research projects that benefit the whole community.
By partnering with Pooch & Mutt to provide accessible consumer testing, we ensure that individual dog owners can make informed decisions about their pet's nutrition. At the same time, vets and professionals have access to the highest-resolution tools needed for complex cases.
This dual approach strengthens the entire ecosystem of gut health from everyday dietary support, to precision veterinary care.
In Summary
For veterinary professionals seeking detailed microbiome data to guide diagnosis, treatment, and advanced nutritional or behavioural strategies, BIOME9’s GutDiscovery® test is the gold standard.
For pet owners looking for reliable general gut health insights and food advice, Pooch & Mutt’s Gut Health Test is a trusted and accessible option.
If you’d like to learn more about integrating GutDiscovery® into your practice or research, please get in touch with Vets@BIOME9.com.
At BIOME9, our mission has always been to push the boundaries of canine gut health research and deliver the best microbiome testing and veterinary support.
Today, we’re excited to announce a new chapter in that journey: a collaboration with Pooch & Mutt.
This fresh new approach will continue to bring accessible, reliable, microbiome testing - paired with the same great supplements and expert advice you trust.
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.
As winter sets in, it’s not just humans who feel the effects of shorter days and colder weather. Our dogs experience seasonal changes too, and with winter comes new challenges for their immune health, digestive balance, and overall wellness. The cooler months are prime time to check in on your dog’s gut health and take simple steps to support their microbiome.
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In our GutDiscovery® report, you will see a few references to the ‘resilience’ of your dog’s Gut Microbiome. But what actually is resilience in the context of gut health, how is it measured, and why is it so important?
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Does your dog go through bouts of itching, or seem unwell after meals, and you aren’t sure if it's an allergy or intolerance? Knowing the difference between the two may be the key to your dog’s comfort.
In a ground-breaking new partnership, Guide Dogs UK has teamed up with BIOME9 to explore and optimise the gastrointestinal health of their puppies as they train to be guide dogs.
There are many tools to help manage our dogs' behaviour, such as training and physical activity. However, did you know that the microbiome is an underused resource in addressing unwanted behaviours and even influencing your dog's anxiety and stress levels?
