Assessment of the effects of dietary fibre and animal-derived fermentable substrates on the gastrointestinal microbiome and associated faecal parameters of the domestic cat (Felis catus) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand

Appendix 1 is reproduced under a Creative Commons Attribution 4.0 International (CC BY 4.0) license as: Butowski CF, Thomas DG, Young W, Cave NJ, McKenzie CM, Rosendale DI, & Bermingham EN. (2019.) Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal microbiome and organic acid profiles of the domestic cat (Felis catus). PLOS ONE, 14(5):e0216072. https://doi.org/10.1371/journal.pone.0216072Globally, commercial diets high in animal protein and fat are becoming increasingly popular for pets. However, there is little research assessing the impacts of such diets in domestic cats. Dietary fibre and animal-derived fermentable substrates (ADFS) are of interest because of their role in gastrointestinal health. A series of in vivo and in vitro studies were conducted to determine the effects of ADFS on the food-host-microbiome interaction in the domestic cat. Initially, the impact of dietary fibre inclusion in a high protein raw meat diet on the faecal microbiome was determined (Chapter Two). Observations from this study suggested that a high protein raw meat diet was highly digestible and influenced the frequency of defecation in the domestic cat. As part of this study, I also assessed two methodologies. Firstly, the point at which the faecal microbiome should be sampled after diet adaption (Chapter Three) and secondly, the suitability of a rectal swab sample (Chapter Four) in determining the composition of the faecal microbiome. I ascertained that the faecal microbiome of the cat could ferment dietary fibre (inulin and cellulose). Furthermore, relative stability of the microbiome was reached after day 5. However, rectal swab samples did not replicate the taxonomic complexity of the faecal microbiome. Based on results from Chapter Two, I assessed the fermentative capacity of a range of ADFS compared to dietary fibre in vitro (Chapter Five). I found that hydrolysed collagen produced the greatest concentrations of butyrate in this system. Therefore, in the final study, I assessed the impacts of hydrolysed collagen inclusion in a high protein raw meat diet on the faecal metagenome (Chapter Six). Additionally, I assessed tryptophan metabolites as they include a key neurotransmitter, serotonin, which has local effects on the colon and may explain the differences in defecation frequency observed. I found that the hydrolysed collagen was fermented by the gastrointestinal microbiome of the domestic cat and could have the potential to replace dietary fibre in the diet of the domestic cat. From this, future research could verify the potential of ADFS in replacing dietary fibre in domestic cats. In addition, further work is required in determining the functional potential of the microbiome of the domestic cat to fully understand the impact of diet on the host-microbiome interactions