Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the faecal microbiome of growing kittens

Despite being obligate carnivores, cats are fed a wide range of dietary macronutrients within commercial diets. Little is known regarding the feline gastrointestinal microbiome and how it is impacted by diet. Using 16S RNA analysis, changes in diet (protein:carbohydrate ratio) do affect fecal microbiota of growing kittens. However, to investigate potential functional differences deep Illumina shotgun sequencing is required and a study of microbial structure and function in these animals is reported here. This is the largest and most comprehensive analysis of the feline gastrointestinal microbiome to date. It provides an overview of the taxa and gene functions present and how they are impacted by the dietary protein: carbohydrate ratio. The more diverse structure of the high-protein diet might reflect a more specialized microbiome. As anticipated, our permutation approach reduced the number of pathways to a more manageable set. The reduced data set identified six pathways readily interpretable to the study design.