Next-generation DNA sequencing of oral microbes at the Sir John Walsh Research Institute: technologies, tools and achievements

The human oral cavity is home to one of the most diverse, dynamic and complex collections of microbes (the ‘oral microbiota’) with an estimated 700–1,000 different microbial species inhabiting a variety of ecological niches, such as the teeth, tongue, gums and saliva. Despite decades of research, much is still unknown of the functions and activities of the oral microbiota as many species, particularly those discovered by culture-independent (molecular) techniques, are yet to be cultivated. The past decade has seen the introduction of so-called next-generation DNA sequencing (NGS) technologies which can generate unprecedented amounts of DNA sequence data quickly and reliably. NGS has revolutionised the study of oral microbiota by allowing microbial community profiling in health and disease. Furthermore, NGS facilitates the cost-effective sequencing of individual microbial genomes. Over the past 10 years, our research groups have collaborated on a variety of NGS projects involving whole-genome sequencing of a variety of oral and non-oral bacteria, and oral microbiota profiling in health and disease (severe dental caries and periodontal disease). This paper aims to provide an overview of the NGS technologies we have used and the bioinformatic tools available to analyse NGS-scale datasets, and to highlight some of our NGS achievements.