Waltham Catalogue for the Canine Gut Microbiome: A complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery

Background: Over a number of decades, research into canine health and wellbeing has led to substantial findings in key areas such as management of disease, growth, and aging. To date, the majority of microbiome research and databases has been focused on environmental, rodent and human samples giving biases to databases and to interpretation of other species. Given the emergence of the microbiome as a key driver of health and disease, we aimed to produce the most comprehensive catalogue of the gut microbiome of dogs giving novel insights into the functional role of the microbiome in dogs.Results: We generated 1,031 dereplicated metagenome-assembled genomes (MAGs) from canine fecal samples collected across Europe and the USA. From these MAGs, we describe 89 novel species, 10 novel genera and 982 novel strains. This allowed us to profile an independent dataset at mapping rates of 94%, with 32.6 % of reads mapping to novel species. A comprehensive analysis of functional data uncovered 4,182 orthologous gene groups and gives a new view of carbohydrate metabolism capacity of the canine gut microbiome with the discovery of 244 carbohydrate active enzymes spread across a vast range of bacterial species. Collectively, our data demonstrates the canine microbiome is distinct, presumably having evolved to its host, diet and environment over several millennia.Conclusions: We have generated the most complete catalogue to date of the canine gut microbiome at taxonomic and functional levels giving a resource to all researchers in the field, uncovering many novel taxa, and giving insights into the functional role of the canine microbiome to the canine host.