Tackling the canine microbiome in chronic enteropathy: characterising the functionally significant changes that occur with remission of disease

Dogs are the most popular companion animal in Australia, with over 4.2 million pet dogs. Gastrointestinal diseases are commonly diagnosed in dogs, with chronic enteropathy (CE) a group of disorders that causes gastrointestinal tract inflammation. Although the exact cause is not known, dysregulation of the resident gut microbiota has been implicated in development and/or exacerbation of CE.

Microbiomic community profiling using universal biological markers (primarily the 16S rRNA gene) coupled with high throughput sequencing has been used to assess bacterial phyla in a wide variety of vertebrates, including dogs with CE. Although this approach is powerful, it has to date demonstrated few consistent biological differences associated with canine CE, other than a general loss in species richness and diversity.

However, CE is largely an inflammatory condition and a major limitation with current research is that it examines all bacteria rather than only those bacteria recognized by the host immune response.

Additionally, it is the functional capacity of these organisms (determined by their gene repertoires) and not their taxonomic identity that defines their niche within the microbiome. It may well be that despite variation in the taxonomic structure of the microbiome among individuals the functional niches occupied by these various species may be static and consistent.

This longitudinal clinical study will functionally characterise the faecal microbiome through an integrative ‘omics approach: metagenomics, transcriptomics and metabolomics and bacteria coated with immunoglobulins. This will provide a better understanding of the significance of the changes of the microbiota and potentially identify therapeutic targets.