A new study has revealed just how complex and unique the canine gut microbiome is, offering the most detailed picture yet of the bacteria living inside our furry friends’ gut.
The new research led by scientists at the Waltham Petcare Institute moves past earlier work that relied mainly on human data and limited reference libraries, offering more clarity on canine microbes.
Using data from the Mars Petcare archive, the team studied the DNA found in 501 faecal samples collected from 107 healthy dogs across the USA and Europe.
The process produced 5,753 metagenome-assembled genomes (MAGs), consolidated into 1,031 distinct strains. Of those, 982 are novel, 89 are new species and 10 are new genera.
The team's analysis revealed a core set of bacterial species that make up most of the microbes found in healthy dogs. This breakthrough reveals that the canine gut microbiome is truly unique, and it cannot be likened to other species.
Many of the newly discovered bacterials strains produce important enzymes and metabolites that could be capable of influencing the immune system or providing nutrition to cells in the gut lining.
These include, for example, CAZymes—enzymes that break down complex dietary fibres. The prevalence of CAZymes in a number of known species in the canine gut has, for the first time, revealed the critical role of the gut microbiome in dog digestion.
The research also found that a high percentage of metabolic pathways were linked to carbohydrate metabolism, confirming that dogs rely on their microbiome to process certain nutrients.
However, the team also investigated whether the microbiome could be harmful. Using AMRFinderPlus, a tool designed to detect antimicrobial resistance (AMR), stress and virulence genes, the researchers tested the novel bacteria for signs of pathogenicity.
They found that most of the newly discovered bacteria were commensal, meaning they live in the gut without causing any harm, and lacked toxin or AMR genes.
This new discovery dramatically increases knowledge of this important community of microorganisms, which are essential for dogs’ metabolism, immunity and defense.
Dr Gregory Amos, Senior Research Manager at Waltham, said: “With our new, critical understanding of what makes the canine gut microbiome unique, we have never been better equipped to develop solutions that improve the lives of dogs.”
The Waltham Catalogue for the Canine Gut Microbiome is now available as a resource for researchers worldwide, and it can be applied across breeds, ages, sexes, and geography.
Ultimately these new insights could lead to more personalized care for dogs, tailored to their unique biological needs.
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Reference
Castillo-Fernandez, J., Gilroy, R., Jones, R. B., Honaker, R. W., Whittle, M. J., Watson, P., & Amos, G. C. A. (2026). 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, 14(1), 25. https://doi.org/10.1186/s40168-025-02265-w