Emerging trends in genome integration tools for precision engineering of diverse bacterial species

Abstract The ability to precisely insert DNA payloads into a genome enables the comprehensive engineering of cellular phenotypes and the creation of new biotechnologies. To achieve such modifications, the most widely used techniques rely on a host cell’s native DNA repair mechanisms like homologous recombination, which hampers their broader use in organisms lacking these capabilities. Here, we explore the current landscape of genome integration systems with a particular focus on those that function in bacteria and which are precise, self-contained and portable, placing minimal requirements on the host cell. Through a historical analysis, we observe long-term use of recombineering technologies, a recent rise in the use of CRISPR-guided systems that consist of associated integrase machinery, and growing efforts to modify non-model organisms. Looking forward, we highlight some of the remaining challenges and how synthetic genomics may offer a way to create bacterial strains optimised for extensive long-term modification. As the field of synthetic biology sets its sights on real-world impact, the effective engineering of genomes will be critical in shaping the robust phenotypes that applications demand.