[Advances and applications of microbial genome evolution engineering].

Genome evolution during the domestication of an antibiotic-producing Streptomyces strain

The domestication of Streptomyces species for antibiotic production involves long-term, iterative mutagenesis and selection, yet the genomic changes driving enhanced production remain unclear. Analysis of five strains from an industrial lineage of Streptomyces clavuligerus using comparative genomics, transcriptomics an...

CRISPR-Enhanced Microbial Consortia for Pollutant Degradation: Molecular Dynamics-Guided Enzyme Stabilization and Metabolic Pathway Optimization

Novel research is proposed to optimize a pollutant-degrading microbial consortium by employing two state-of-the-art technologies. These technologies will incorporate CRISPR-Cas9-based genome editing in conjunction with molecular dynamics (MD) guided enzyme stabilization methods into one unified product. Both technologi...

Programmable enzymes for targeted gene insertion.

Methods for the Evasion of Restriction-Modification Systems During Genetic Engineering of Fusobacterium Species.

This chapter describes strategies to evade RM defenses and improve transformation efficiencies across diverse Fusobacterium lineages, employing a sequence-based "RM-silencing" method that has enabled successful delivery of replicative plasmids, linear recombination templates, and transposon cassettes into previously in...

Unbiased and scalable reduction of diverse bacterial genomes

The development and application of Stochastic Lineage-based Iterative Minimization (SLIM) is shown, providing a modular, high-throughput platform for unbiased genome reduction across phylogenetically diverse bacteria and establishing a scalable, generalizable framework for navigating the vast landscape of minimized gen...

Population diversity and accelerated mutation drive anaerobic bacterial adaptation during long-term solvent stress

ABSTRACT Experimental evolution can uncover general mechanisms by which microorganisms adapt to environmental stress. Here, we investigate evolutionary trajectories of the anaerobic, lignocellulose-fermenting bacterium Lachnoclostridium phytofermentans ISDg (family Lachnospiraceae) during >2,000 generations of automate...