Credit: Dmytro Koplyk from Pexels

Researchers at the Waltham Petcare Science Institute in the UK recently revealed a complete taxonomic and functional catalog of the canine gut microbiome after analyzing samples from 107 healthy dogs across the U.S. and Europe. The study, published in the journal Microbiome, unveiled an array of new bacterial strains and their role in gut health. The resulting catalog is now the most comprehensive resource for the gut microbiome in companion animal research.

The lack of data for pet microbiomes

Despite a rising interest in the microbiome among scientists and the general public, research on the microbiome of pets, like cats and dogs, remains limited. Unsurprisingly, most research has focused instead on the human microbiome and the microbiome of food production animals, to a lesser degree. Because there is an overlap in some bacteria that reside in the guts of humans and canines, prior studies have often focused on similarities or links to the human microbiome, instead of the functional role of the canine microbiome and how it relates to their health.

This has left a large knowledge gap in the taxonomy and function of the canine gut microbiome, which the research team involved in the new study set out to address. They say a large portion of the canine gut microbiome remains unknown, with only 25% of canine metagenomic sequencing reads mapping to known genomes.

"Without the increased database granularity provided by novel species discovery and appropriate description of the roles of these organisms with a focus on the host in question, our understanding of the canine gut microbiome is inherently limited," the study authors write.

Phylogenetic tree of all recovered MAGs at species taxonomic level with assigned GTDBtk bacterial phylum denoted by colored range. Inner heatmap shows candidate novel taxa at the genus and species levels (blue). Outer heatmap shows relative abundance levels of the 240 species in an independent dataset of 47 dogs (cohort 4). Credit: Microbiome (2026). DOI: 10.1186/s40168-025-02265-w

A comprehensive view into the microbiome of healthy dogs

The dogs involved in the study came from a range of different countries and different living environments, including environmentally enriched kennel facilities at the Waltham Petcare Science Institute and the Pet Health and Nutrition Center and the homes of clients of Mars Veterinary Health and employees of Mars Petcare. Using 501 fecal samples from these dogs, the team conducted both long-read and short-read shotgun metagenomic sequencing. A total of 5,753 metagenome-assembled genomes (MAGs) were reconstructed, which were then dereplicated to 1,031 strains.

Of these strains, 982 were found to be new canine-specific strains, 89 were novel species, and 10 were novel genera. Mapping rates improved greatly, to 95% from only around 25% with previous databases.

The team says the most abundant species found was Prevotella copri , at 8.1%, which is, interestingly, also the most abundant bacterium in the gut microbiome of humans. Some newly identified species were found to have key roles in carbohydrate metabolism, short-chain fatty acid and vitamin production and bile acid metabolism.

The team also notes that all novel discovered species were found to be commensal, meaning they live in the gut, but do not affect the host, neither significantly harming nor helping. The researchers posit that a lack of pathobionts and pathogens is expected given the healthy cohort.

Better understanding leads to better canine health

The results of the new study are a boon for canine health. The catalog can be used as a resource to study microbiome changes in disease, aging and dietary interventions, and also enables more precise development of probiotics, prebiotics, and dietary strategies for dogs. The work has also provided a useful baseline for antimicrobial resistance in healthy dogs.

The study authors write, "The taxa and functions presented here provide the highest resolution image of the healthy pet dog microbiome to date. By providing the MAGs themselves as well as details on their taxonomic lineage and functional annotation, this resource can be used by all researchers working on canines across breed, age, sex, or geography, expanding opportunities to understand the role of the microbiome in canine health and disease, as well as more completely map the taxonomic and functional impact of dietary interventions."

Written for you by our author Krystal Kasal, edited by Gaby Clark, and fact-checked and reviewed by Robert Egan—this article is the result of careful human work. We rely on readers like you to keep independent science journalism alive. If this reporting matters to you, please consider a donation (especially monthly). You’ll get an ad-free account as a thank-you.

Publication details

Juan Castillo-Fernandez et al, 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). DOI: 10.1186/s40168-025-02265-w

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Citation: Largest canine gut microbiome catalog reveals hundreds of new bacterial strains (2026, January 21) retrieved 21 January 2026 from https://phys.org/news/2026-01-largest-canine-gut-microbiome-reveals.html

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