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.

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.

Microbes provide a diverse source of functional traits that can be used to address a whole range of human and environmental problems, from agriculture and farming, to human and wildlife health, and energy production and climate change mitigation. Although microbes and their derivatives have been used for decades in some contexts, recent advances in sequencing and other technologies have allowed us to identify and understand novel sources and applications. Here, we review a range of different types of microbial biotechnology, including probiotics or microbial inputs, prebiotics, enzybiotics, microbiome transplants, antimicrobial peptides and secondary metabolites, across a range of contexts including human health, agriculture, biofuel production and wildlife disease, among others. We discuss the advances made in these fields, along with the complexities and problems associated with success. We also comment on ethical issues surrounding the use of microbial biotechnology and areas of policy and risk assessment that will need to develop to promote safe implementation.