The discipline of synthetic biology aims to domesticate and standardize DNA parts, modularize cellular processes, and construct synthetic organisms for specific applications. Recent advances in DNA design, synthesis, and assembly have enabled the construction of synthetic DNAs of whole-genome size. However, building designer organisms from scratch is still challenging due to the need for large-scale DNA synthesis and extensive genetic engineering. The use of cell-free biology, which employs cell extracts or purified proteins and cofactors, is gaining popularity but lacks scalability. Microbes, including engineered strains, are widely used in industrial processes, and while random mutagenesis and adaptive laboratory evolution (ALE) can optimize strains, they are not always beneficial and can lead to scale-up failures.
Researchers are moving away from the dichotomy of model and non-model organisms and exploring the diversity of wild-type microorganisms, which may perform better for certain products. With the availability of whole-genome sequencing and high-quality reference genomes, researchers can now expand beyond traditional model organisms and explore the utilization of non-model microorganisms. Synthetic biology tools, such as standardized DNA assembly and genome manipulation, enable the rapid establishment of new microbial systems, and high-throughput technologies, such as transcriptome, proteome, and metabolome profiling, facilitate large-scale data generation.