Non-model microbes and microbial communities: opportunities for biotechnology

Microbiology research is expanding from model species to non-model species and from studying single-species phenotypes to microbiomes and emergent functions. Here, we review the biotechnological opportunities brought forward by this expansion. Omics and automation have expanded the catalogue of non-model microbes that can be used in biotechnology, either on their own or as modules for assembling synthetic communities. The latter offer a complementary or alternative approach to monocultures due to their high resilience, single-step processing of complex substrates and suitability for open-environment applications. We also review the tools for engineering model and non-model microorganisms and communities, namely, targeted genome editing, adaptive laboratory evolution and ecological engineering. Going forward, increased focus on non-model microbes and methods for designing synthetic communities is needed to unlock the potential of the rich functional repertoire of non-model organisms and microbial communities.