The search for an understanding of the causal elements that lead to neurodegenerative diseases has motivated researchers for decades. Today, Alzheimer's disease is the most prevalent form of dementia and affects approximately fifty million people worldwide, with only 5% of patients carrying causal genetic mutations. In recent years, studies of animal models as well as observations in humans have brought the gut microbiome to the forefront of AD research, as a significant contributor to the development of Alzheimer's disease. In fact, the gut microbiome is now understood to be a modulator of health and disease in numerous areas of physiology, including energy metabolism, immunity, endocrinology, and most relevant to this thesis, brain health and cognition. The gut microbiome is a complex environment composed of symbiotic bacteria, fungi and viruses (the microbiota) that produce a wide range of signalling molecules that are interpreted both by members of the microbiota and by the host (the microbiome). The host-gut interface is an ecosystem that consists of bi-directional signals and pressures applied by both constituents in order to maintain symbiotic homeostasis. Significant deleterious effects on health occur when homeostasis is lost, which may take place due to a variety of factors. These include host genetic factors and environmental factors, such as diet. Modulation of the gut microbiome has become a potentially viable therapeutic avenue for Alzheimer's disease, though it currently remains at the early stage of discovery. In this thesis, I characterize the evolution of Alzheimer's disease in the 5xFAD mouse model, with a focus on the gut microbiome and on cognitive decline and brain biochemistry. Gut microbiota modulaiton was implemented using germ-free and low-complexity bacterial cocktails, in which I outline the effects microbiota modulation on hallmarks of AD and provide insights into the metabolite profile of the brain altered by the microbiota and AD. The work in this thesis was equally motivated by the development of diagnostic tools using microscopy techniques. Biochemical assessments of disease status and progression provide information pertaining to "what" is interacting and "how much" this affects disease. With microscopy, we may gain the additional knowledge of "where" physiological constituents are and how they interact with the surrounding environment. I describe a novel multi-modal microscopy pipeline that enables the observation of signals of interest in large volumes and at high resolution with a capacity to cross-reference regions of interest in both modalities. The pipeline, known as gutOPT, consists of a sample preparation workflow compatible with mesoscale optical projection tomography (OPT) of fluorescently-labelled targets and subsequent imaging of pre-selected regions of interest in high-resolution modalities, such as confocal microscopy.