A review of the application of CRISPR-Cas in microbial biotechnology

Abstract

Today, the use of CRISPR-Cas systems for genome editing and modification in diverse microbial species is widespread. Originally identified as bacterial defense mechanisms against viral invaders, CRISPR-Cas systems are present across a broad spectrum of microbial taxa, including bacteria and archaea. These systems are categorized into two main classes: Class 1, comprising multi-subunit protein complexes, and Class 2, distinguished by single-unit Cas protein systems such as Cas9. The flexibility of CRISPR-Cas systems stands out as one of their most attractive features. Various genome editing approaches employed by Class 1 and Class 2 systems reflect their high adaptability in defense mechanisms, which confer protection against viral infections. Furthermore, CRISPR-Cas systems contribute to the stability and integrity of bacterial and archaeal genomes. Currently, these systems serve as essential tools in laboratories for functional genomics, precise genome editing, and targeted gene programming. They play a key role in biotechnology, especially in the engineering of microorganisms for environmental remediation and biofuel production. Beyond laboratory applications, CRISPR-based diagnostics enable rapid and accurate detection of infections and genetic variations, thus facilitating early disease diagnosis. Moreover, the development of targeted antimicrobial strategies utilizing CRISPR has found extensive application in combating drug-resistant microorganisms. Collectively, CRISPR-Cas systems have become indispensable tools in microbial genome engineering and in the advancement of innovative diagnostic and therapeutic approaches in medicine. In this review, data were collected and analyzed through a literature search in Springer, ScienceDirect, Scopus, and John Wiley databases from 2018 to 2025, using MeSH-defined keywords related to microbial CRISPR-Cas systems.