The human microbiome has been studied in some form for over three hundred years, but in the last decades sequencing technologies have provided a new way to study it. This chapter gives an overview of the microbiome, emphasising an epidemiological perspective. First, it introduces the microbiome in broad biological terms. It explains some different types of microbiome study and covers the two main classes of sequencing approach used to investigate it: amplicon sequencing (usually the 16S rRNA gene) and metagenomic sequencing. The chapter explores the strengths and limitations of each type of sequencing data and offers guidance for which to choose for a study. A case study of the effect of antibiotics on the gut microbiome investigates a real dataset, introducing some common analysis techniques such as diversity statistics and ordinations, as well as encouraging critical thinking about the scientific implications of the results. Finally, the chapter summarises important considerations for epidemiological studies that include a microbiome component.