In relation to human health and well-being, strategies that positively influence the composition and activity of the microbiota are keenly sought, and diet is widely accepted as being a major factor for altering the gastrointestinal microbiota. The overarching aim of my Ph.D. studies was to characterize how diets with varying profiles of carbohydrate content and intake affect the gut and the oral microbiota of healthy individuals. Two key groups of subjects were used in separate studies: elite male athletes (endurance walkers) and healthy conventional subjects. During my studies, advances in DNA sequencing (and related bioinformatics methods) have enabled transition from the taxonomic profiling of microbial communities, to the production of data representing their collective genetic potential (i.e. the metagenome). As such, I have used both approaches here, and provide new insights into the nature of the diet x microbiota interactions in healthy individuals. Chapter One reviews literature relating to diet x microbiota interactions with specific reference to how some diets (such as low FODMAP) affect the gut microbiota. Chapter Two provides the methodological details shared across the other research Chapters, and that samples either stored at sub-optimal temperatures, or that undergo repeated freeze-thaw cycles, are depleted of bacteria with a Gram-negative cell wall ultrastructure (e.g. Bacteroidetes, Proteobacteria). These results emphasized the importance of sample preservation and storage on these types of data generated from stool samples. Chapters Three and Four presents my results and conclusions about how the dietary pattern of elite race walkers during their period of intensified training affected their oral and stool microbiota, respectively. This research was undertaken in complement to the Supernova 1 study coordinated by Australian Institute of Sports. Stool and saliva samples were collected at the beginning and end of a three-week dietary intervention period, from elite male endurance race walkers choosing to consume either a High Carbohydrate (HCHO), High Carbohydrate-periodised (PCHO) or a Low Carbohydrate High Fat (LCHF) diet, and the microbial communities were examined using 16S rRNA amplicon sequencing. The results in Chapter Three show that the LCHF diet results in substantive changes in v Publications during candidature Published, peer-reviewed review article