The microbes that live in and on our bodies play major roles in health and disease due to their symbiotic relationship with the host. Understanding how these communities adapt to changes in their environment - either by natural or anthropological forces - is currently a critical area of research for improving holistic healthcare. The aim of this thesis was to demonstrate the potential of large-scale shotgun-sequenced ancient dental calculus to study the wider diversity of the oral microbiome. In Manuscript A, I have shown that ancient dental calculus can be used to improve the understanding of past human oral microbiome diversity, after analysing the largest and oldest ancient dental calculus dataset to date. In this manuscript I also present new tools to help improve authentication of ancient microbiomes. Manuscript B describes the repository AncientMetagenomeDir, a community-level resource that lists all public ancient metagenomic sequencing datasets. The resource will allow researchers to efficiently re-use public data to ensure the robusticity and improve the statistical power of future studies. Manuscript C presents an entirely rewritten user-friendly palaeogenomics pipeline following latest software development and bioinformatics best practices. The pipeline nf-core/eager, has been developed in a way that allows for easy integration with large scale computing infrastructure required for such analyses. Importantly, I have extended this genomics pipeline to have in-parallel metagenomic profiling and screening of ancient DNA characteristics. These manuscripts have contributed new insights into the biology and evolution of oral biofilms, but also introduced new open-source and sustainable tools and resources that will allow further investigation of ancient microbiomes.