1. Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome.
- Author
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Lam KN, Spanogiannopoulos P, Soto-Perez P, Alexander M, Nalley MJ, Bisanz JE, Nayak RR, Weakley AM, Yu FB, and Turnbaugh PJ
- Subjects
- Animals, CRISPR-Associated Protein 9 metabolism, Escherichia coli growth & development, Feces microbiology, Female, Gene Expression Regulation, Bacterial, Mice, Inbred BALB C, Mice, Transgenic, Proof of Concept Study, Mice, Bacteriophage M13 genetics, CRISPR-Associated Protein 9 genetics, CRISPR-Cas Systems, Chromosome Deletion, Chromosomes, Bacterial, Clustered Regularly Interspaced Short Palindromic Repeats, Escherichia coli genetics, Gastrointestinal Microbiome, Gene Editing
- Abstract
Mechanistic insights into the role of the human microbiome in the predisposition to and treatment of disease are limited by the lack of methods to precisely add or remove microbial strains or genes from complex communities. Here, we demonstrate that engineered bacteriophage M13 can be used to deliver DNA to Escherichia coli within the mouse gastrointestinal (GI) tract. Delivery of a programmable exogenous CRISPR-Cas9 system enables the strain-specific depletion of fluorescently marked isogenic strains during competitive colonization and genomic deletions that encompass the target gene in mice colonized with a single strain. Multiple mechanisms allow E. coli to escape targeting, including loss of the CRISPR array or even the entire CRISPR-Cas9 system. These results provide a robust and experimentally tractable platform for microbiome editing, a foundation for the refinement of this approach to increase targeting efficiency, and a proof of concept for the extension to other phage-bacterial pairs of interest., Competing Interests: Declaration of interests K.N.L., P.S., and P.J.T. are listed inventors on a US provisional patent application related to this work (33167/55262P1). P.J.T. is on the scientific advisory boards for Kaleido, Pendulum, and SNIPRbiome. All other authors declare no competing interests., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
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