Genetic toolbox development for engineering Bacteroides and other bacterial species

Engineering bacteria to address human health challenges has been an active and productive area of research for many decades. Historically, a major emphasis of this work has been on modifying laboratory-adapted species to generate chemical or biological compounds for therapeutic use or for further study. In recent years, however, there has been a growing interest in utilizing nonmodel commensal and probiotic bacterial strains for development as in situ engineered living therapeutic or diagnostic machines. While substantial insight can be gained from previous work in well-studied organisms such as Escherichia coli, effective genetic and metabolic manipulation of novel species often requires novel tools. Here, we highlight strategies for the development of synthetic biology toolboxes for nonmodel bacterial strains to assist researchers across disciplines in establishing the molecular biology framework required to work with relatively understudied species. We focus on advances in engineering the Bacteroides genus as an example of how to establish such a pipeline.