Plasmid-mediated
antibiotic-free fermentation holds significant
industrial potential. However, the requirements for host elements
and energy during plasmid inheritance often cause cell burden, leading
to plasmid loss and reduced production. The stable maintenance of
plasmids is primarily achieved through a complex mechanism, making
it challenging to rationally design plasmid-stabilizing strains and
characterize the associated genetic factors. In this study, we introduced
a fluorescence-based high-throughput method and successfully screened
plasmid-stabilizing strains from the genomic fragment-deletion strains
of Escherichia coli MG1655 and Bacillus subtilis 168. The application of EcΔ50 in antibiotic-free fermentation increased the
alanine titer 2.9 times. The enhanced plasmid stability in EcΔ50 was attributed to the coordinated deletion of
genes involved in plasmid segregation and replication control, leading
to improved plasmid maintenance and increased plasmid copy number.
The increased plasmid stability of BsΔ44 was due to the deletion of the phage SPP1 surface receptor
gene yueB, resulting in minimized sporulation, improved
plasmid segregational stability and host adaptation. Antibiotic-free
fermentation results showed that strain BsΔyueB exhibited a 61.99% higher acetoin titer compared to
strain Bs168, reaching 3.96 g/L. When used for the
fermentation of the downstream product, 2,3-butanediol, strain BsΔyueB achieved an 80.63% higher
titer than Bs168, reaching 14.94 g/L using rich carbon
and nitrogen feedstocks. Overall, our work provided a plasmid-stabilizing
chassis for E. coli and B. subtilis, highlighting their potential for antibiotic-free
fermentation of valuable products and metabolic engineering applications.