Two major outstanding questions in microbiome research ask what microbes are present in a community and how they interact with each other and their hosts. Recent, rapid improvements in nucleic acid (DNA and RNA) sequencing allow us to study the composition and function of microbiomes in unprecedented detail, leading to a step change in our understanding of host–microbe interactions. This chapter gives a broad overview of the basic toolkit available to modern microbiologists and microbial ecologists, exploring their application to key questions about microbiome structure and function. We cover tools based on nucleic acid sequencing (e.g. amplicon sequencing, metagenomics, metatranscriptomics) as well as approaches targeting larger molecules such as metabolomics and proteomics. We discuss the use of microbial culture as a means of measuring functional capacity of individual microbes, or building artificial communities to understand emergent properties of consortia. We emphasise the advantages of combining multiple techniques alongside robust experimental design to garner powerful quantitative estimates of microbiome structure, and how this relates to host–microbe interactions.