Computational design of CRISPR guide RNAs to enable strain-specific control of microbial consortia.

ABSTRACT: Microbes naturally coexist in complex, multistrain communities. However, extracting individual microbes from and specifically manipulating the composition of these consortia remain challenging. The sequence-specific nature of CRISPR guide RNAs can be leveraged to accurately differentiate microorganisms and facilitate the creation of tools that can achieve these tasks. We developed a computational program, ssCRISPR, which designs strain-specific CRISPR guide RNA sequences with user-specified target strains, protected strains, and guide RNA properties. We experimentally verify the accuracy of the strain specificity predictions in both Escherichia coli and Pseudomonas spp. and show that up to three nucleotide mismatches are often required to ensure perfect specificity. To demons

SUBMITTER: Rottinghaus AG 

PROVIDER: S-EPMC9910470 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature