Exploring Unknown Feline and Canine -omes and their Health Implications

Abstract

Recent advances in omics technologies have allowed comprehensive research on a biological system at various levels from genes to metabolites. Indeed, an extensive body of research has been conducted in humans as well as laboratory and production animals, targeting diverse biological entities, such as microbiome and metabolome, using omics technologies. However, research into such -omes has only begun recently in companion animals, mainly focusing on densely populated microbial communities, notably the gut and skin microbiota. This trend indicates a need for further epidemiological research into characterising unknown or underexplored -omes and investigating their health implications in companion animals.

The present thesis aims to contribute towards addressing this knowledge gap firstly by characterising the feline urinary microbiome and metabolome and the feline and canine gut resistome using different omics technologies and secondly by investigating their association with urinary tract diseases or environmental factors. This thesis consists of five chapters, including three epidemiological studies utilising omics data. Chapter 1 provides a brief review of omics concepts and technologies, the principles of epidemiological research employing omics data, and the outline of this thesis. Then, each of the following three chapters presents each epidemiological study. Study 1 (Chapter 2) and Study 2 (Chapter 3) are designed as case-control studies among cats attending first-opinion veterinary clinics in Hong Kong. Study 1 shows for the first time through 16S rRNA gene sequencing that cats harbour distinct microbial communities in their bladder, disproving the traditional belief that urine is sterile in healthy cats. Furthermore, it reveals that cats with chronic kidney disease likely have a similar microbial community structure to cats with Escherichia coli cystitis, suggesting that cats with chronic kidney disease may require close monitoring for the development of cystitis by this genus. Study 2 identifies and quantifies metabolites in feline urine to an unprecedented extent through untargeted metabolomics and shows that, while the urinary metabolome is not associated with cats' urinary tract disease status, a significant level of metabolome clustering is possible among cats under the same environmental exposure. This study also shows no statistically significant compositional similarity between the feline urinary microbiome and metabolome. Study 3 (Chapter 4) characterises the canine and feline gut resistome based on publicly available shotgun metagenomic sequence data generated by previous two dietary intervention studies. It reveals that increased protein and reduced carbohydrates in the diet are associated with increased antibiotic resistance gene diversity in canine and feline gut microbiota. Chapter 5 concludes this thesis by discussing the implications of its findings and challenges.

The present thesis characterises feline and canine -omes that have been believed to be non-existent or have been underexplored, investigates their associations with the health of the animals or environmental factors, and discusses the validity of these associations for causality. Its findings are novel and suggest the needs and directions for future research targeting these biological entities.

Date of Award	11 Jan 2022
Original language	English
Awarding Institution	City University of Hong Kong
Supervisor	Dirk Udo PFEIFFER (Supervisor) & Rodrigo BICALHO (External Co-Supervisor)