4 Feb 2026
Paper, published in Microbiome, details investigation by scientists from the Waltham Petcare Science Institute into the canine microbiome through meta-genomic sequencing.
Chris Simpson
Job Title
Image: Artur / Adobe Stock
A new study has provided a major boost to our understanding of the canine microbiome, researchers say.
The paper, published in Microbiome, details an investigation by scientists from the Waltham Petcare Science Institute into the canine microbiome through meta-genomic sequencing.
Drawing on data from Mars Petcare, researchers used a combination of long-read and short-read sequencing on 501 faecal samples from 107 healthy dogs from across the UK, US and France.
The scholars were able to reconstruct 5,753 meta-genome assembled genomes, consolidated into 1,031 distinct strains.
That included 982 new canine-specific strains, 89 novel species and 10 novel genera, which the authors described as “an unprecedented discovery of novel taxa in the companion animal space”. They found 240 species overall, representing the core canine gut microbiome.
The species are said to account for approximately 83% of the canine gut microbiome, compared with traditional mapping rates around 25%, representing “a dramatic increase in previous knowledge of the canine microbiome” and highlighting the previous knowledge gaps in this space.
Between the newly discovered species and the absence of the Akkermansia muciniphila bacterium – said to play a protective role in the development of cardiovascular disease in both mice and humans – the authors said: “Collectively, this suggests that despite some similarities across mammals, the canine microbiome is distinct, presumably having evolved to its host, diet and environment over several millennia.”
The findings also offered insight into species of bacteria previously not known to be present in the canine gut, such as carbohydrate-active enzymes (CAZymes), which break down complex dietary fibres.
The prevalence of CAZymes is said to have indicated, for the first time, the crucial role that the microbiome plays in dogs’ digestion.
Waltham researchers also investigated whether the reconstructed genomes contained antimicrobial resistance, stress resistance and virulence genes.
While virulence factors were found in four species, three of which were known pathogens, none were found in the novel species, which was said to suggest that all novel discovered species are commensal.
The authors described the paper – titled, “Waltham catalogue for the canine gut microbiome” – as “the most comprehensive microbiome resource in all companion animal research”.
Spanning multiple cohorts of dogs living in different environments across different countries, they said the resource will “provide the highest resolution image of the healthy pet dog microbiome to date” and “can be used by all researchers working on canines across breed, age, sex or geography”.
The researchers hope the findings can help facilitate personalised treatment for dogs tailored to their unique biological needs.
Co-author 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.”
