CRISPR/Cas in food microbial biotechnology: from genome editing to precision microbiology

CRISPR/Cas technologies have opened new opportunities for the precise genetic engineering of microorganisms relevant to food biotechnology. Their programmability enables targeted genome modification, transcriptional regulation, sequence-specific antimicrobial activity, and nucleic acid detection, offering new strategies to improve fermentation processes, microbial safety, and the functional properties of food-associated strains. However, experimental evidence varies considerably across microorganisms and applications, and successful genome editing does not necessarily translate into improved technological performance. This review examines recent advances in CRISPR/Cas-based engineering of starter cultures, probiotic strains, and production microorganisms, alongside emerging strategies for bacteriophage resistance, pathogen and biofilm control, and food diagnostics. Particular emphasis is placed on distinguishing applications experimentally validated in food-related settings from proof-of-concept studies conducted in laboratory or biomedical contexts. The review also evaluates the major barriers to industrial implementation, including strain-specific editing efficiency, genetic stability, process robustness, and validation in food matrices. It also considers the distinct biosafety and regulatory implications of production microorganisms removed or inactivated during processing versus viable engineered cultures retained in final products. By integrating advances in molecular engineering with evidence of functional performance and practical implementation requirements, this review highlights both the opportunities and current limitations of CRISPR/Cas technologies in food microbial biotechnology.