Fig. 5. Future smart design, construction, and applications of minimal genomes.

Synthetic minimal genomes will facilitate the realisation of some of synthetic biology’s founding principles of modularity, computational design, automated building, and data-driven feedback into rational design iterations. a In the design stage, modules are selected from a database containing a variety of functionalities, such as carbon source utilisation, biosynthetic pathways, biosensing and growth-regulating modules. Modelling can then be used to ensure compatibility between modules, simulate metabolic flux, fine tune expression levels, and predict phenotypes or the yields of products. b Assisted by robotic high-throughput cloning and assembly techniques, modules are constructed and integrated into chassis minimal genomes. Multiplexing for design variations and integrations into different minimal genome strain contexts could allow for further optimisation. c The resulting strains could gain versatile functions, from growing on non-conventional feedstocks to producing recombinant proteins, and biosensing. Ultimately, designed minimal-genome strains could be analysed by multi-omics approaches. d The resulting data could feed back to machine learning models, enabling a better understanding of minimal-genome rational design principles, and possibly, using generative AI, design new-to nature minimal genomes.