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The CRISPR-Cas system, derived from the adaptive immune mechanisms of bacteria and archaea, utilizes RNA-guided nucleases to recognize and cleave specific DNA sequences. Nucleases like Cas9 and Cas12 require only a single protein for targeted DNA cleavage, offering intuitive design, a streamlined workflow, and advantages in scalability, parallelism, and versatility. In classic chassis organisms such as E. coli, Bacillus subtilis, Corynebacterium glutamicum, and yeasts, this system has been repeatedly validated as an effective tool for building high-yield strains, synthesizing complex metabolites, enhancing stress tolerance, and optimizing process performance.
Figure 1. Modes of action for various CRISPR–Cas tools. (Benz, F., et al., 2025)
For different microbial strains, Creative Biogene has established methodologies encompassing both exogenous CRISPR systems and endogenous CRISPR systems. These are individually optimized based on the specific genetic background, recombination efficiency, nuclease toxicity sensitivity, and PAM preferences of each microbe. Whether for single-gene knockouts, point mutations, large fragment insertions, pathway replacements, or multiplex editing, we deliver stable, scarless modifications ideal for subsequent fermentation scale-up and further engineering.
01 Gene Knockout (KO)
02 Gene Knock-in (KI) and Targeted Integration
03 Site-Directed Mutagenesis
04 Gene Replacement
05 Multiplex Genome Editing
Our genome editing services cover a broad spectrum of microbial species. For specific industrial or specialized strains, we offer custom CRISPR method development services, providing a one-stop solution from vector design to established editing protocols and final strain construction.
Classic Engineering Chassis
Yeasts and Fungi
Probiotics and Functional Strains
We offer a range of services, including knockouts, knock-ins, point mutations, and fragment replacements. Deliverables vary based on the target strain and design complexity, but typically include:
For standard E. coli gene knockout or knock-in projects, the typical timeline starts from 4-5 weeks. Timelines for other species will be determined based on the specific editing plan.
In a study investigating carbapenem resistance in P. aeruginosa, researchers evaluated the roles of chromosomal β-lactamases and porins in imipenem susceptibility. Creative Biogene constructed a CRISPR-Cas9 knockout strain, OprDKOCR, targeting the oprD gene to validate phenotypic and genotypic findings. The knockout strain was whole-genome sequenced to confirm complete deletion. Using this strain alongside transposon mutants and clinical isolates, the team assessed gene expression, protein function, and antibiotic susceptibility. Creative Biogene's CRISPR-based microbial genome editing service enabled the generation of stable, precisely edited strains suitable for downstream functional and resistance studies.
Figure 2. Imipenem MICs and RNA transcript levels of resistance mechanisms for P. aeruginosa clinical isolates and lab strains. (Freed S Jr, et al. 2024)
In microbial CRISPR engineering, success depends on editing efficiency, precision, and timeline control. Our stable systems are reliable for traditional model strains and easily adaptable to novel chassis, probiotics, and non-model industrial microbes. We excel at challenging edits, including >10 kb fragment manipulation, multi-target designs, toxic sequence replacement, and custom methods using endogenous CRISPR.
This expertise enables efficient, traceable, and scalable microbial genome editing without compromising quality. Whether constructing industrial strains, developing functional microbes, validating metabolic pathways, or creating new CRISPR methods, Creative Biogene provides mature platforms and expert support to advance next-generation microbial engineering.
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