A Landmark Study in Canine Microbiome Science
| Castillo-Fernandez J, Gilroy R, Jones RB, Honaker RW, Whittle MJ, Watson P, Amos GCA. Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery. Microbiome. 2026;14(1):25. DOI: 10.1186/s40168-025-02265-w |
Executive Summary
In January 2026, researchers at the Waltham Petcare Science Institute published the most comprehensive mapping of the canine gut microbiome ever undertaken. This landmark study represents a paradigm shift in our understanding of canine digestive health, identifying 240 core bacterial species that account for over 80% of the healthy canine gut microbiome, along with the discovery of 89 entirely novel species and 10 new bacterial genera unique to dogs.
The study’s significance extends beyond taxonomy. By mapping the functional capabilities of these bacteria, including their roles in short-chain fatty acid production, carbohydrate metabolism, and bile acid transformation, this research establishes the scientific foundation for understanding how nutrition directly influences whole-body health through the gut microbiome.
Key Findings at a Glance
| Metric | Finding |
| Sample Size | 501 faecal samples from 107 dogs (USA & Europe) |
| Core Species | 240 species comprising >80% of gut microbiome |
| Novel Discoveries | 982 new strains, 89 novel species, 10 new genera |
| Mapping Improvement | 25% → 95% of metagenomic reads |
| Butyrate Producers | 37.5% of species (45.6% by abundance) |
| Propionate Producers | 18.8% of species |
| CAZyme Density | 71 carbohydrate-active enzymes per species |
Study Précis: Methods and Design
Background and Rationale
Despite rising interest in the microbiome among scientists and the general public, research on the gut microbiome of companion animals has remained notably limited. Prior to this study, only approximately 25% of canine metagenomic sequencing reads could be mapped to known genomes, leaving a substantial proportion of the canine gut microbiome functionally uncharacterised.
The research team noted that because there is overlap in some bacteria residing in the guts of humans and canines, prior studies often focused on similarities or links to the human microbiome rather than the functional role of the canine microbiome and how it relates specifically to canine health. This approach, the researchers argued, inherently limited our understanding of dog-specific gut health.
Study Cohort and Sample Collection
The study analysed 501 faecal samples from 107 healthy dogs spanning multiple countries across the United States and Europe. Dogs were sourced from diverse living environments, including environmentally enriched kennel facilities at the Waltham Petcare Science Institute and the Pet Health and Nutrition Center, as well as the homes of clients of Mars Veterinary Health and employees of Mars Petcare. This diversity was intentional, ensuring the resulting catalogue would be broadly representative of the healthy canine population.
Sequencing and Bioinformatic Approach
The researchers employed both long-read and short-read shotgun metagenomic sequencing, representing the most sophisticated approach currently available for microbiome characterisation. This dual-technology methodology enabled the reconstruction of 5,753 metagenome-assembled genomes (MAGs), which were subsequently dereplicated to 1,031 distinct bacterial strains.
The use of metagenome-assembled genomes is particularly significant as it allows researchers to reconstruct near-complete bacterial genomes directly from environmental samples, without requiring laboratory cultivation. This approach captures the full diversity of the gut ecosystem, including species that cannot be grown in laboratory conditions.
Taxonomic Discoveries: A New Map of the Canine Gut
Scale of Novel Discovery
The scale of taxonomic discovery achieved by this study is unprecedented in companion animal research. Of the 1,031 strains identified, 982 were found to be new canine-specific strains not previously described in scientific literature. More significantly, the study identified 89 entirely novel bacterial species and 10 novel bacterial genera.
These novel genera belong to bacterial families including Erysipelotrichaceae, Erysipelatoclostridiaceae, Atopobiaceae, Anaeroplasmataceae, Lachnospiraceae, and Anaerovoracaceae. Many of these families are known to be involved in fibre fermentation and short-chain fatty acid production, suggesting these newly discovered organisms play important roles in nutrient processing.
The Core Canine Microbiome
The study defined a core microbiome of 240 bacterial species that collectively account for more than 80% of the bacterial content in healthy canine faeces. This core was validated against an independent dataset of 47 dogs, confirming the robustness and generalisability of these findings.
The most abundant species identified was Prevotella copri, comprising 8.1% of the average canine microbiome. Interestingly, this species is also the most abundant bacterium in the human gut microbiome, though its specific strains and functional roles differ between hosts. Other highly abundant core species included Candidatus Skylacomonas (7.3%) and Candidatus Ileibacterium (5.7%), both of which are now recognised as major contributors to .
Canine Microbiome Distinctiveness
A critical finding with profound implications for nutritional science is that the canine microbiome is fundamentally distinct from the human microbiome. The researchers noted that many human microbiome paradigms cannot be directly applied to dogs.
Most notably, Akkermansia muciniphila, a bacterial species that has received enormous attention in human gut health research for its roles in metabolic health and gut barrier function, was completely absent from all canine samples. This finding definitively demonstrates that dogs have evolved their own unique gut ecosystem, with distinct bacterial populations adapted to canine physiology, diet, and immune systems.
| MAPPING IMPROVEMENT 25% → 95% Metagenomic reads now mappable to known canine-specific genomes |
Functional Analysis: What the Microbiome Actually Does
Beyond simply cataloguing which bacteria are present, the study provided unprecedented insight into what these bacteria actually do. This functional annotation transforms our understanding from a mere inventory to a mechanistic framework for understanding gut health.
Short-Chain Fatty Acid Production
Short-chain fatty acids (SCFAs), particularly butyrate, propionate, and acetate, are bacterial fermentation products that serve as signalling molecules throughout the body, influencing everything from gut barrier integrity to brain function, immune regulation to metabolic health.
The study found that 37.5% of species possess genes for butyrate production. When weighted by abundance, this rises to 45.6% of the microbiome by abundance, meaning nearly half of the bacterial mass in a healthy canine gut is actively capable of producing this critical metabolite. An additional 18.8% of species can produce propionate.
Butyrate serves as the primary energy source for colonocytes (cells lining the colon), maintains gut barrier integrity, reduces inflammation, and has been shown to influence distant organs including the brain (via the gut-brain axis), the liver (via the gut-liver axis), and the immune system (via the gut-immune axis). The finding that such a substantial proportion of the canine microbiome is dedicated to butyrate production underscores the centrality of SCFA metabolism to canine health.
Carbohydrate Metabolism: Compensating for Canine Limitations
One of the study’s most significant findings relates to carbohydrate metabolism. Dogs possess limited genetic capacity for digesting complex carbohydrates compared to omnivores and herbivores. The gut microbiome, the study reveals, compensates extensively for this limitation.
Species in the canine gut microbiome possess an average of 71 carbohydrate-active enzymes (CAZymes) per species. This enzymatic density enables the breakdown of diverse fibre types that dogs cannot digest independently.
Carbohydrate Degradation Capacity
| Substrate Type | % of Species Capable |
| Chitin | 75% |
| Hemicellulose | 37% |
| Cellulose | 36% |
| Starch | 22% |
This finding has profound implications for nutrition: dietary fibre diversity directly supports microbial diversity and function. Different bacterial species specialise in breaking down different fibre types, meaning a varied fibre profile in the diet supports a more complete microbial ecosystem.
Bile Acid Metabolism: The Gut-Liver Connection
A particularly significant discovery was the identification of two novel Peptacetobacter species with the capacity to convert primary bile acids to secondary bile acids. The researchers described this as “an important finding in the context of chronic GI disease in pets.”
These bacteria possess bile salt hydrolase (BSH) enzymes and the bai operon, the genetic machinery required for 7α-dehydroxylation, the critical step in secondary bile acid synthesis. Secondary bile acids, including deoxycholic acid and lithocholic acid, serve multiple functions: they protect against pathogenic bacteria, regulate liver metabolism, influence glucose homeostasis, and serve as signalling molecules affecting distant organs.
This finding illuminates the gut-liver axis at a mechanistic level, demonstrating that specific gut bacteria directly regulate hepatic function through bile acid metabolism.
Amino Acid Biosynthesis
The study found that 42% of species contained complete lysine biosynthesis pathways, contributing to amino acid availability for the host. This finding suggests the microbiome plays a role in protein nutrition beyond simple digestion, actively synthesising amino acids that the host can utilise.
Safety Profile of Novel Species
All 89 novel species identified in the study were confirmed to be commensal organisms, showing no known virulence factors. The researchers noted that the absence of pathobionts and pathogens was expected given the healthy cohort, but this finding nonetheless confirms that the newly discovered species are normal inhabitants of the healthy canine gut rather than opportunistic invaders.
Implications for Canine Nutrition
The study’s authors explicitly noted that “dietary interventions” show “promising results in modulating aspects of canine GI function.” The extensive functional characterisation provided by this research establishes nutrition as a primary lever for supporting gut health and, through the gut’s connections to other organ systems, whole-body health.
Dietary Fibre: Fuel for the Microbiome
With 71 carbohydrate-active enzymes per species and the capacity to break down cellulose, hemicellulose, starch, and chitin, the canine gut microbiome is designed to process diverse plant fibres. The study validates an approach to canine nutrition that prioritises prebiotic fibre diversity to fuel beneficial bacterial populations.
Different fibre types support different bacterial populations, meaning dietary diversity translates directly to microbial diversity. A diet rich in varied plant-based ingredients provides the substrates necessary for a complete, functioning gut ecosystem.
SCFA Production and Whole-Body Health
The finding that nearly half the microbiome by abundance produces butyrate positions SCFA production as a central metric of gut health. Dietary interventions that support SCFA-producing bacteria, primarily through provision of fermentable fibres, have cascading effects throughout the body.
Butyrate influences the gut-brain axis (affecting mood, cognition, and stress response), the gut-immune axis (regulating inflammatory responses), the gut-liver axis (modulating hepatic metabolism), and the gut-skin axis (influencing dermal health). Propionate regulates gluconeogenesis and appetite, while acetate serves as a substrate for lipogenesis and energy production.
The Case for Canine-Specific Formulation
Perhaps the most important nutritional implication of this research is the definitive demonstration that human microbiome paradigms cannot be directly applied to dogs. The complete absence of Akkermansia muciniphila, despite its prominence in human gut health research, exemplifies this point.
This finding argues strongly for canine-specific nutritional formulation based on canine-specific research, rather than extrapolation from human studies. The Waltham catalogue now provides the scientific foundation for precisely this approach.
Validation of the Bonza ‘One Gut. Whole Dog.’ Positioning
The findings of the Waltham catalogue provide compelling scientific validation for Bonza’s core positioning: “One Gut. Whole Dog.” This section examines how the study’s discoveries substantiate each element of this framework.
The Gut as Command Centre: Scientific Validation
The study demonstrates that the gut microbiome is not merely a digestive organ but a metabolic and signalling hub with influence extending throughout the body. The functional annotation reveals bacteria producing:
Short-chain fatty acids that serve as signalling molecules affecting brain function (gut-brain axis), immune regulation (gut-immune axis), liver metabolism (gut-liver axis), and inflammatory status throughout the body.
Secondary bile acids through the newly discovered Peptacetobacter species, directly regulating hepatic function and glucose metabolism.
Amino acids through complete biosynthesis pathways, contributing to protein nutrition and cellular function.
This is precisely what “One Gut. Whole Dog.” asserts: that gut health is the foundation upon which whole-body health is built.
Gut-Organ Axes: Now Mapped at the Species Level
Bonza’s educational content has long emphasised the gut-brain, gut-immune, gut-liver, gut-skin, and gut-joint axes. The Waltham catalogue now provides species-level evidence for these connections:
| Axis | Waltham Catalogue Evidence |
| Gut-Brain | 45.6% abundance dedicated to butyrate production; butyrate crosses blood-brain barrier, modulates neuroinflammation |
| Gut-Liver | Novel Peptacetobacter species with BSH enzymes and bai operon for bile acid metabolism |
| Gut-Immune | SCFA production supports regulatory T-cell development and inflammatory modulation |
| Gut-Skin | SCFA anti-inflammatory effects extend to dermal tissue via systemic circulation |
| Gut-Joint | Butyrate’s anti-inflammatory properties influence systemic inflammatory status affecting joint health |
Nutrition as the Primary Lever: Confirmed
The study’s explicit statement that “dietary interventions” show “promising results in modulating aspects of canine GI function” directly validates Bonza’s premise that nutrition is the primary tool for supporting gut health.
The extensive carbohydrate-processing capacity of the microbiome (71 CAZymes per species, with capabilities spanning cellulose, hemicellulose, starch, and chitin) demonstrates that plant-based fibres are precisely what the canine gut microbiome is equipped to process. This finding supports Bonza’s formulation philosophy of providing diverse prebiotic fibres through plant-based ingredients.
Canine-Specific Science: The Foundation
Bonza has consistently emphasised the importance of canine-specific research rather than solely relying on extrapolation from human studies. The Waltham catalogue powerfully validates this approach by demonstrating:
1. The canine microbiome is fundamentally distinct from the human microbiome, with over 900 canine-specific strains identified.
2. Key species prominent in human gut health research (notably Akkermansia muciniphila) are entirely absent in dogs.
3. Dogs have evolved their own unique gut ecosystem, requiring dog-specific approaches to nutrition and health.
This is precisely the scientific foundation upon which Bonza’s formulations are built.
The Waltham catalogue’s most consequential finding for dog owners is that diet is the most powerful lever available for shaping which bacterial populations thrive in the canine gut. Plant-based diets, properly formulated, deliver the fibre diversity that drives the fibre-fermenting capacity and short-chain fatty acid production this catalogue characterises. For the full peer-reviewed evidence on how plant-based canine nutrition translates the Waltham findings into measurable health outcomes, see the Bonza evidence review on plant-based dog food research.
Conclusion: A New Era in Canine Gut Science
The Waltham catalogue represents a watershed moment in canine microbiome science. By providing the most comprehensive mapping of the canine gut microbiome to date, identifying 240 core species and 89 novel species, and characterising their functional capabilities in unprecedented detail, this research establishes the scientific foundation for evidence-based approaches to canine gut health.
For Bonza, this study serves as independent, peer-reviewed validation of our core positioning. The science confirms:
The gut is indeed a command centre for whole-body health, with bacterial metabolites influencing distant organs through multiple gut-organ axes.
Nutrition is the primary lever for modulating gut function, with dietary fibre diversity directly supporting microbial diversity and function.
Canine-specific science matters, as the dog microbiome is fundamentally distinct from human paradigms.
One Gut. Whole Dog. is not a marketing slogan—it is a scientific reality, now mapped at the species level by the world’s leading pet nutrition research institution.
| “The taxa and functions presented here provide the highest resolution image of the healthy pet dog microbiome to date.” — Castillo-Fernandez et al., Microbiome 2026 |