CRISPR screens in the era of microbiomes

Abstract : Recent advances in genomics have uncovered the tremendous diversity and richness of microbial ecosystems. New functional genomics methods are now needed to probe gene function in high-throughput and provide mechanistic insights. Here, we review how the CRISPR toolbox can be used to inactivate, repress or overexpress genes in a sequence-specific manner and how this offers diverse attractive solutions to identify gene function in high-throughput. Developed both in eukaryotes and prokaryotes, CRISPR screening technologies have already provided meaningful insights in microbiology and host-pathogen interactions. In the era of microbiomes, the versatility and the functional diversity of CRISPR-derived tools has the potential to significantly improve our understanding of microbial communities and their interaction with the host.