The most diverse and most densely populated habitats in human are the gut and the oral cavity. While these environments are anatomically distinct and each provide a different environment to microorganisms, their interplay has significant implications for human health and disease. The oral cavity, as the primary gateway to the gastrointestinal tract, facilitates microbial transfer to the gut, shaping downstream microbial communities. However, high-throughput and taxonomic refined analyses of the oral microbiome is lacking behind. Therefore, this project focusses on enhancing the taxonomic and functional characterisation on oral bacteria in relation to human health.