Our knowledge and understanding of the structure and function of complex host-associated communities has grown exponentially in the last decade through improvements in sequencing technologies. Despite this, there are still many outstanding research questions, which will undoubtably lead to many more. Concerted effort is required to elucidate the composition and function of taxonomic groups other than bacteria that constitute host microbiomes, and to extend our current cataloguing efforts to non-model and field-based host organisms. Further to this, we need to continue to move beyond the 'who?' question provided by relatively cheap amplicon sequencing to gain a better understanding of 'what?' the microbiome is doing, using metatranscriptomics approaches. Critically, we need to understand how members of the microbiome interact to confer function. Given the current unprecedented environmental change, microbiome plasticity may prove vital to host resilience and fitness. Furthermore, there is considerable potential for microbial biotechnology to improve numerous aspects of humanity, although care must be taken to ensure environmental and social justice prevail.

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.

A classic example of microbiome function is its role in nutrient assimilation in both plants and animals, but other less obvious roles are becoming more apparent, particularly in terms of driving infectious and non-infectious disease outcomes and influencing host behaviour. However, numerous biotic and abiotic factors influence the composition of these communities, and host microbiomes can be susceptible to environmental change. How microbial communities will be altered by, and mitigate, the rapid environmental change we can expect in the next few decades remain to be seen. That said, given the enormous range of functional diversity conferred by microbes, there is currently something of a revolution in microbial bioengineering and biotechnology in order to address real-world problems including human and wildlife disease and crop and biofuel production. All of these concepts are explored in further detail throughout the book.