Abstract

   Companion animals provide an excellent model for studies of the gut
   microbiome because potential confounders such as diet and environment
   can be more readily controlled for than in humans. Additionally,
   domestic cats and dogs are typically neutered early in life, enabling
   an investigation into the potential effect of sex hormones on the
   microbiome. In a longitudinal study to investigate the potential
   effects of neutering, neutering age and gender on the gut microbiome
   during growth, the faeces of kittens (16 male, 14 female) were sampled
   at 18, 30 and 42 weeks of age. DNA was shotgun sequenced on the
   Illumina platform and sequence reads were annotated for taxonomy and
   function by comparison to a database of protein coding genes. In a
   statistical analysis of diversity, taxonomy and functional potential of
   the microbiomes, age was identified as the only factor with significant
   associations. No significant effects were detected for gender,
   neutering, or age when neutered (19 or 31 weeks). At 18 weeks of age
   the microbiome was dominated by the genera Lactobacillus and
   Bifidobacterium (35% and 20% average abundance). Structural and
   functional diversity was significantly increased by week 30 but there
   was no further significant increase. At 42 weeks of age the most
   abundant genera were Bacteroides (16%), Prevotella (14%) and
   Megasphaera (8%). Significant differences in functional potential
   included an enrichment for genes in energy metabolism (carbon
   metabolism and oxidative phosphorylation) and depletion in cell
   motility (flagella and chemotaxis). We conclude that the feline faecal
   microbiome is predominantly determined by age when diet and environment
   are controlled for. We suggest this finding may also be informative for
   studies of the human microbiome, where control over such factors is
   usually limited.

Introduction

   In the last decade, advances in DNA sequencing technologies have
   accelerated the culture-independent study of microbial communities and
   improved our understanding of the microbiome (the combined genetic
   material of a community and the functional potential of its protein
   coding genes). One area of particular interest is the human microbiome
   and its relevance to health, disease and nutrition. The finding that
   the microbiome is often a better predictor of complex metabolic
   diseases (such as diabetes, cardiovascular disease and obesity) than
   genetic markers [[33]1,[34]2] underpins its importance to health. A
   wide variety of factors has been shown to be associated with the gut
   microbiomes of healthy individuals including diet [[35]3], age [[36]4]
   and gender [[37]5]. In addition associations with a wide range of
   diseases such as obesity [[38]6], type 1 diabetes [[39]7] and even
   autism [[40]8] have been reported. With few exceptions [[41]9,[42]10],
   studies in humans are generally observational. Intervention studies are
   typically carried out in rodent models and have demonstrated causal
   relationships between diet, the microbiome and obesity [[43]11].

   The microbiome of companion animals is of interest for a number of
   reasons. Owners share their home with their pets and an exchange of
   microbes between pets and owners has been demonstrated [[44]12].
   Furthermore, companion animals can suffer from a range of medical
   conditions such as obesity, cardiovascular disease, diabetes and
   periodontal disease, for which microbial associations have been
   demonstrated in humans. Microbiome research in companion animals to
   date includes but is not limited to the skin of allergic dogs [[45]13],
   the gingiva of dogs with periodontal disease [[46]14], the faeces of
   dogs with diarrhoea and inflammatory bowel disease [[47]15] as well as
   the effect of dietary macronutrients [[48]16,[49]17] and fibre [[50]18]
   on the faecal microbiome in cats.

   Companion animals may be more suitable for studying some aspects of the
   microbiome than humans. Complete and balanced diets may be fed as the
   sole source of food for extended periods of time, reducing confounding
   effects of different dietary preferences between individuals.