New Research Maps the Dog Gut Microbiome—Implications for Canine Nutrition

January 22, 2026

Quick Summary: A landmark study from the Waltham Petcare Science Institute has created the most comprehensive catalog of the canine gut microbiome ever assembled. The research identified nearly 1,000 previously unknown bacterial strains and revealed that dogs' guts are dominated by fiber-fermenting bacteria—the same species that thrive in humans. These findings add to growing evidence that dogs are well-equipped to derive nutrition from plant-based ingredients.

The Study at a Glance

In January 2026, researchers at the Waltham Petcare Science Institute (part of Mars Petcare) published a major study in the peer-reviewed journal Microbiome. The research team, led by Juan Castillo-Fernandez, set out to address a significant gap in veterinary science: despite growing interest in the microbiome, only about 25% of bacteria in the canine gut had been previously identified.¹

The study analyzed fecal samples from 107 healthy dogs across the United States and Europe, representing dogs from various living environments—including both kennel facilities and private homes. Using advanced metagenomic sequencing techniques, the researchers reconstructed 5,753 bacterial genomes, which were then refined to 1,031 distinct strains.¹

Key findings:

982 bacterial strains newly documented in dogs
89 entirely novel species identified
10 novel genera discovered
Mapping accuracy improved from ~25% to 95%¹

The resulting "Waltham Catalogue" is now the most comprehensive resource for canine gut microbiome research available.

The Surprising Bacteria Dominating Your Dog's Gut

One of the study's most notable findings was the identification of the most abundant bacterial species in healthy dogs: Prevotella copri, present at 8.1% abundance.¹

Why is this significant? Prevotella copri is a fiber-fermenting bacterium—it specializes in breaking down complex carbohydrates from plant foods. It's also the most abundant species in the human gut microbiome.¹

This discovery aligns with previous research showing that the canine gut microbiome is more similar to the human microbiome than to pigs or mice.² A 2018 study published in Microbiome found that dogs and humans share significant overlap in gut bacteria composition, and that diet has a substantial, reproducible effect on the canine microbiome regardless of breed or sex.²

The dominance of fiber-fermenting bacteria in dogs is consistent with the evolutionary history of canine domestication. Dogs have lived alongside humans for thousands of years, sharing our increasingly plant-rich diets. Genetic research has identified specific adaptations in dogs—including increased copies of the AMY2B gene for starch digestion—that distinguish them from wolves and enable efficient plant nutrient processing.³

How Diet Shapes the Canine Microbiome

The newly identified bacterial species in this study were found to play key roles in carbohydrate metabolism, short-chain fatty acid (SCFA) production, vitamin synthesis, and bile acid metabolism.¹ These functions are directly influenced by what dogs eat.

Research consistently demonstrates that fiber-rich diets promote beneficial changes in the canine gut:

Increased beneficial bacteria: Studies show that when dogs consume diets higher in vegetable fiber, they experience increases in Firmicutes (a phylum that includes many beneficial species) and decreases in potentially problematic bacteria like Fusobacteria and Proteobacteria.⁴

Short-chain fatty acid production: Fiber-fermenting bacteria produce SCFAs including butyrate, acetate, and propionate. These compounds support gut barrier function, reduce inflammation, and provide energy for intestinal cells.⁵ A 2025 study published in mSystems found that dietary fiber significantly altered both the microbiome composition and metabolite production in dogs, with individualized responses suggesting that the benefits of fiber may be personalized.⁶

Prebiotic effects: Various plant fibers have been studied for their prebiotic properties in dogs. Research has shown that ingredients like beet pulp and potato fiber can positively shift microbiome composition toward beneficial bacteria.⁴⁷

In contrast, research on raw meat-based diets has shown different microbiome patterns. Dogs fed high-protein, low-fiber raw diets tend to show decreases in fiber-fermenting bacteria like Faecalibacterium and Prevotella—genera associated with SCFA production and carbohydrate digestion.⁴

What This Means for Canine Nutrition

This research does not prove that any single diet is "best" for all dogs—nutrition science rarely offers such simple conclusions. However, the findings contribute to a growing body of evidence with important implications:

Dogs are not obligate carnivores. The microbiome profile revealed in this study—dominated by fiber-fermenting bacteria capable of processing complex carbohydrates—is not what we would expect to see in a species that evolved exclusively on meat. This is consistent with the scientific classification of dogs as omnivores or facultative carnivores.⁸

The gut microbiome responds to diet. What dogs eat directly shapes which bacteria thrive in their digestive systems. Fiber-rich diets appear to promote bacteria associated with beneficial metabolic functions, while very low-fiber diets show different microbial patterns.

Baseline data enables future research. As the study authors note, this 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."¹

Limitations and Context

In the interest of scientific transparency, it's worth noting several important caveats:

This was an observational study. The research characterized the microbiome of healthy dogs but did not test specific dietary interventions or health outcomes.

Correlation is not causation. While the abundance of fiber-fermenting bacteria suggests dogs are equipped to process plant nutrients, this alone doesn't prove any particular diet is optimal.

Individual variation matters. The dogs in this study came from different backgrounds and presumably different diets. The 2025 mSystems study on fiber response in dogs found significant individual variation, suggesting that microbiome benefits may be somewhat personalized.⁶

The study was conducted by Mars Petcare researchers. While published in a peer-reviewed journal, readers should be aware of the research funding source. The findings are consistent with independent research on canine microbiomes, but industry funding is always worth noting.

The Bottom Line

The Waltham Catalogue represents a significant advancement in our understanding of what lives inside dogs' digestive systems. The dominance of fiber-fermenting bacteria—particularly Prevotella copri, the same species most abundant in humans—adds to evidence that dogs have evolved to efficiently process plant-based nutrients.

For pet parents interested in plant-based or plant-forward nutrition for their dogs, this research provides scientific context for understanding how the canine digestive system processes fiber, carbohydrates, and plant proteins. Properly formulated diets that include these ingredients appear to work with, rather than against, the natural microbial ecosystem in dogs' guts.

As always, any significant dietary changes should be made gradually and ideally in consultation with a veterinarian, especially for dogs with specific health conditions.

References

Castillo-Fernandez J, 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
Coelho LP, Kultima JR, Costea PI, et al. Similarity of the dog and human gut microbiomes in gene content and response to diet. Microbiome. 2018;6:72. DOI: 10.1186/s40168-018-0450-3
Axelsson E, Ratnakumar A, Arendt ML, et al. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature. 2013;495:360-364.
Pilla R, Suchodolski JS. The role of the canine gut microbiome and metabolome in health and gastrointestinal disease. Frontiers in Veterinary Science. 2020;6:498.
Wernimont SM, Radosevich J, Jackson MI, et al. The effects of nutrition on the gastrointestinal microbiome of cats and dogs: Impact on health and disease. Frontiers in Microbiology. 2020;11:1266.
Response of the gut microbiome and metabolome to dietary fiber in healthy dogs. mSystems. 2025. DOI: 10.1128/msystems.00452-24
Panasevich MR, Kerr KR, Dilger RN, et al. Modulation of the faecal microbiome of healthy adult dogs by inclusion of potato fibre in the diet. British Journal of Nutrition. 2015;113(1):125-133.
Bosch G, Hagen-Plantinga EA, Hendriks WH. Dietary nutrient profiles of wild wolves: Insights for optimal dog nutrition? British Journal of Nutrition. 2015;113(S1):S40-S54.

This article summarizes peer-reviewed research for educational purposes. Petaluma is committed to transparency in how we discuss the science of canine nutrition. For questions about whether a plant-based diet is appropriate for your individual dog, please consult with your veterinarian.