Fig. 4

Exploitation of endogenous and engineered CRISPR-Cas systems in bacteria. Exogenous DNA sequences can be targeted by CRISPR-Cas systems to build up phage resistance in food starter cultures (to vaccinate yoghurt strains against bacteriophage), to prevent the uptake and dissemination of plasmids that encode undesirable traits such as antibiotic resistance genes (to immunize probiotic strains used in dietary supplements), or to ensure the genetic integrity and genomic homeostasis of valuable cultures (to fend off mobile genetic elements such as transposons and prophages) (upper panels). Unique records of iterative vaccination events captured as a series of spacers in CRISPR arrays can be used as sequencing targets for the detection, monitoring and typing of strains of interest, which include food cultures, spoilage organisms or pathogens (center panels). By contrast, self-targeting and engineered applications can be used in industrial settings to improve industrial workhorses by genome editing (indicated by ‘scissors’ symbol), or by re-directing the metabolic flux of various pathways for synthetic and yield purposes (lower panels). Lethal self-targeting can also be harnessed for the select eradication of pathogens or contaminants of interest. CRISPRa CRISPR activation, CRISPRi CRISPR interference