Entering the 21st century, major advancements in biotechnology, such as CRISPR/Cas [1] and omics technologies [2], have substantially empowered microbes to produce chemicals through complex pathways [3]. Our understanding and capabilities in metabolic engineering using model organisms have advanced considerably, allowing us to identify the remaining challenges that must be overcome to achieve commercially viable production in certain conditions. Recognizing these obstacles, substantial efforts have been made to address them. Moreover, alternative approaches, such as using nonmodel organisms with specific advantages in certain contexts, are gaining increasing attention 1, 4, 5.

Among these, Pseudomonas putida KT2440 (hereafter P. putida), Halomonas bluephagenesis TD01 (formerly Halomonas sp. TD01, hereafter H. bluephagenesis), and Zymomonas mobilis ZM4 (hereafter Z. mobilis) are demonstrating potential in industrial applications. All three have been evaluated in pilot-scale production, with H. bluephagenesis expected to reach full-scale production of short-chain-length polyhydroxyalkanoates (scl-PHAs) by the end of 2024 (PhaBuilder data, Figure 1).

This review introduces the current status and history of industrial applications for these three representative nonmodel microorganisms, followed by their metabolic characteristics and genome engineering tools. Our aim is to offer insights that support future research in optimizing these organisms for industrial applications and inform the selection of new microbial hosts.