Koch’s postulates originally proposed a one microorganism–one disease approach to disease; however, it is now clear that many diseases of plants and animals are associated with changes in the taxonomic composition and function of the microbiome, and that health and disease are mediated by a dynamic interplay between host factors, environmental factors, the host microbiota and pathogenic microorganisms. Commensal microbes can become pathogenic under certain conditions, and disease can arise from complex polymicrobial infections. Although causation and correlation can be difficult to untangle, it is clear that the host microbiome plays a key role in resisting colonisation by pathogens across all host taxa, from plants to animals to humans. This offers exciting possibilities for manipulating microbiomes in order to reduce pathogenic infection in a range of contexts, including agriculture, wildlife and human health, through the use of probiotics, prebiotics and microbiome transplants, among other approaches.

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.