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  • Review Article
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De novo design of synthetic microbial genomes

Nature Reviews Bioengineering (2026)Cite this article

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Abstract

Synthetic biology enables the bottom-up synthesis of microbial genomes through the assembly of synthetic DNA fragments. Such de novo genome synthesis could enable the generation of synthetic cells, with applications in fundamental biology, biotechnology and biomedicine. In this Review, we explore the rational design of synthetic microbial genomes, including expression unit optimization, codon usage, transcriptional and translational control, and RNA and protein turnover. We then examine genome-level design considerations, highlighting the roles of chromosome architecture, gene orientation and positioning, and 3D gene arrangement, outlining strategies for the assembly and testing of synthetic genomes. Finally, we propose a path towards a fully realized synthetic cell, emphasizing the importance of method integration, including evolution-based strategies and machine learning.

Key points

  • Bottom-up synthetic genomes can be built with genes of diverse microbial and viral origins to investigate genome design principles.

  • The design of genes and their regulatory elements for synthetic genomes involves a trade-off between complexity and the range of achievable expression levels.

  • The architecture of natural genomes is only partially understood and should thus be carefully considered in the design and testing of synthetic genomes.

  • Computer-aided design, step-by-step testing and laboratory evolution of functional modules are important approaches to realize a functional synthetic genome.

  • Different conditions and applications require different synthetic genome designs.

  • Lessons from synthetic genome design are not only applicable to the bottom-up synthetic cell field but are also valuable in bioengineering applications.

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Fig. 1: Design–build–test–learn cycle for synthetic cells.
Fig. 2: Trade-off between complexity and effect on expression range of regulatory mechanisms.
Fig. 3: Different layers of gene architecture.
Fig. 4: Functionalization strategies for synthetic genomes.

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Acknowledgements

The authors gratefully acknowledge L. Olivi for critically reading the manuscript. This publication is part of the project “Evolving life from non-life (EVOLF)” (SUMMIT.1.004, N.J.C., T.J.G.E., J.v.d.O.) of the research programme SUMMIT, which is financed by the Dutch Research Council (NWO) and “BaSyC – Building a Synthetic Cell” Gravitation grant (024.003.019, J.v.d.O.) of the Netherlands Ministry of Education, Culture and Science (OCW) and the Netherlands Organisation for Scientific Research (NWO).

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  1. These authors contributed equally: Charlotte C. Koster, Henrique da Costa Oliveira.

Authors and Affiliations

  1. Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands

    Charlotte C. Koster, Henrique da Costa Oliveira, Fabian van Beveren, Joep Houkes, Jolien J. E. van Hooff, Thijs J. G. Ettema, John van der Oost & Nico J. Claassens

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  1. Charlotte C. Koster
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Contributions

C.C.K., H.d.C.O., F.v.B. and J.J.E.v.H. contributed to discussion of content, researching data for the article, and writing and editing of this manuscript. J.H. researched data for the article and contributed to editing and reviewing of this manuscript. T.J.G.E., J.v.d.O. and N.J.C. contributed to discussion of content, reviewing, and editing the manuscript before submission.

Corresponding author

Correspondence to Nico J. Claassens.

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Competing interests

J.v.d.O. is an advisor for NTrans Technologies, Scope Biosciences and Hudson River Biotechnology. N.J.C. is an advisor for Farmless and Novya Biotech. These companies were not involved in this work and had no influence on the content of this article. The other authors declare no competing interests.

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Koster, C.C., da Costa Oliveira, H., van Beveren, F. et al. De novo design of synthetic microbial genomes. Nat Rev Bioeng (2026). https://doi.org/10.1038/s44222-026-00410-0

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