Ground Breaking New Study Reveals the True Complexity of the Canine Microbiome

For humans and animals alike, a healthy gut microbiome is central to countless physiological processes in the body.¹ Defined as the community of microorganisms that live in the digestive tract, including bacteria and archaea, the gut microbiome is essential for metabolism, immunity and defense against pathogens. 
 

But, despite its importance, the gut microbiome in dogs is vastly understudied. Our understanding is primarily based on human-centric research.  And this lack of species-specific insight has limited how much we have been able to monitor, support and influence gut health in dogs.  

That is, until now.  

A new standard in pet microbiome research

Waltham scientists have now uncovered how unique the canine gut microbiome really is.  

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Waltham Catalogue for the Canine Gut Microbiome: A complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery has been published this month in Springer Nature's Microbiome.

The most comprehensive resource of its kind, the catalogue dramatically increases what was previously known about the canine gut microbiome.  

Dogs' true uniqueness revealed 

The discovery began with metagenomic sequencing, performed on 501 faecal samples from 107 healthy dogs across the USA and Europe. This was made possible by data leveraged from the Mars Petcare archive.  

The process produced 5,753 metagenome-assembled genomes (MAGs), consolidated into 1,031 distinct strains. 

Of those 1,031 distinct strains: 
 

• 982 are novel  
• 89 are new species  
• 10 are new genera 
   

This breakthrough reveals that the canine gut microbiome is truly unique. It cannot be likened to other species, which challenges prior assumptions.  

Uncovering the critical role of the gut microbiome in dogs 

Through the catalogue's detailed functional descriptions of the novel strains, we can better understand their role in the health of dogs. We've learnt that many of them produce important enzymes and metabolites, that could be capable of influencing the immune system or providing nutrition to cells in the gut lining. 

Moreover, we have gained insights into known species of bacteria, that we previously did not know were present in the canine gut. Like 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 dogs' digestion. 

And the high percentage of metabolic pathways attributed to carbohydrate metabolism, confirms dogs rely on their microbiome to process certain nutrients.  

A better view of canine gut microbial capabilities 

But despite the beneficial roles of the canine gut microbiome, could it also cause harm? This question was important to answer, given the microbiome's potential for pathogenicity – it's ability to cause disease.  

To investigate, we used AMRFinderPlus, a tool that can identify if bacteria possess antimicrobial resistance (AMR), stress or virulence genes.  

Importantly, we found that most of the novel bacteria in the canine gut microbiome were commensal and lacked toxin or AMR genes.  

Shaping more personalised care for dogs 

The Waltham Catalogue for the Canine Gut Microbiome is now a key resource for researchers worldwide.  

Spanning multiple cohorts of pet dogs, across different countries, living in different environments – the catalogue provides the highest resolution image of the healthy dog microbiome to date.  

Researchers will be able to apply the catalogue's insights regardless of the dog breed, age, sex or geography. 
 

As a result, the catalogue expands opportunities to understand the role of the microbiome in canine health and disease. And it is a step towards more completely mapping the taxonomic and functional impact of dietary interventions.  

Powerfully, the insights could unlock a future of personalised treatment for dogs, tailored to their unique biological needs. 

Dr Gregory Amos, Senior Research Manager at Waltham, reflects on the significance of this: '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.' 

By driving these new discoveries, Waltham continues to advance science in service of our purpose: Build A Better World for Pets. 

Source: Waltham

Reference
1 Barko et al., 2018