RT Journal Article
SR Electronic
T1 Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiota
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.07.09.193847
DO 10.1101/2020.07.09.193847
A1 Kathy N. Lam
A1 Peter Spanogiannopoulos
A1 Paola Soto-Perez
A1 Margaret Alexander
A1 Matthew J. Nalley
A1 Jordan E. Bisanz
A1 Feiqiao B. Yu
A1 Peter J. Turnbaugh
YR 2020
UL http://biorxiv.org/content/early/2020/07/09/2020.07.09.193847.abstract
AB The recognition that the gut microbiome has a profound influence on human health and disease has spurred efforts to manipulate gut microbial community structure and function. Though various strategies for microbiome engineering have been proposed, methods for phage-based genetic manipulation of resident members of the gut microbiota in vivo are currently lacking. Here, we show that bacteriophage can be used as a vector for delivery of plasmid DNA to bacteria colonizing the gastrointestinal tract, using filamentous phage M13 and Escherichia coli engrafted in the gut microbiota of mice. We employ M13 to deliver CRISPR-Cas9 for sequence-specific targeting of E. coli leading to depletion of one strain of a pair of fluorescently marked isogenic strains competitively colonizing the gut. We further show that when mice are colonized by a single E. coli strain, it is possible for M13-delivered CRISPR-Cas9 to induce genomic deletions that encompass the targeted gene. Our results suggest that rather than being developed for use as an antimicrobial in the gut microbiome, M13-delivered CRISPR-Cas9 may be better suited for targeted genomic deletions in vivo that harness the robust DNA repair response of bacteria. With improved methods to mitigate undesired escape mutations, we envision these strategies may be developed for targeted removal of strains or genes present in the gut microbiome that are detrimental to the host. These results provide a highly adaptable platform for in vivo microbiome engineering using phage and a proof-of-concept for the establishment of phage-based tools for a broader panel of human gut bacteria.Competing Interest StatementKNL, PS, and PJT are listed inventors on a U.S. provisional patent application related to this work (33167/55262P1). PJT is on the scientific advisory boards for Kaleido, Pendulum, Seres, and SNIPRbiome. All other authors declare no competing interests.