Host-Microbe Interactions in Health and Disease, and Survey of Antimicrobial Resistance of Bacteria Isolated from Retail Meat

The human gut microbiome confers many benefits to its host, therefore dysbiosis; an imbalance in microbial community composition, may have a negative impact on health. It is unclear however if dysbiosis is a consequence of a particular disease process, or a cause. This thesis explores the influence of gut microbiome on health outcomes and disease progression in the context of dietary fibre consumption and obesity, and peritoneal dialysis in patients with chronic kidney disease. This thesis also investigates the correlation between Crohn’s disease (CD) and genes expressed exclusively by blood monocytes in reponse to bacteria. Finally, this thesis explores antimicrobial resistance in bacteria isolated from retail chicken and pork meat sold in the Australian Capital Territory (ACT) and New South Wales (NSW).