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.