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) Sutterella and (B) Clostridium compared 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.

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)

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Cohabitation and shared ASVs (16S)

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Gut-brain axis

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AMR and the shared resistome

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Oncology and therapy response

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