Characterization, complete genome sequencing, and CRISPR/Cas9 system-based decontamination of a novel Escherichia coli phage TR1 from fermentation substrates

Phage contamination has become a major concern for industrial bacteria, such as Escherichia coli BL21(DE3), used in fermentation processes. Herein, we report CRISPR/Cas9 defense system-based strategy to precisely prey and degrade phage DNA decontaminate target phages. First, isolated novel from substrates with BL21(DE3) the host, named TR1. It showed typical podovirus morphology head diameter of 51.46 ± 2.04 nm tail length 9.31 2.77 nm. The burst size TR1 was 151 PFU/cell, suggesting its strong fecundity system. Additionally, whole-genome sequencing revealed that genome 44,099 bp 43.8% GC content, encoding total 68 open reading frames. Comparative genomics phylogenetic analysis designated this be new species genus Christensenvirus . To counteract TR1, employed constructed two phage-resistant E. strains, BL21-C BL21-T, based on conserved genes. Both EOP assays growth curves indicated resistance recombinant without affecting cell growth. Therefore, study aimed provide resilient respond ever-changing phages ongoing phage–host arm race environments by personalized design spacers CRISPR/Cas system-containing plasmid. More importantly, our research sparks use mechanism prevent extensive biotechnological applications.