Engineering modular viral scaffolds for targeted bacterial population editing

Bacteria are central to human health and disease, but existing tools to edit microbial consortia are limited. For example, broad-spectrum antibiotics are unable to precisely manipulate bacterial communities. Bacteriophages can provide highly specific targeting of bacteria, but assembling well-defined phage cocktails solely with natural phages can be a time-, labor- and cost-intensive process. Here, we present a synthetic biology strategy to modulate phage host ranges by engineering phage genomes in Saccharomyces cerevisiae. We used this technology to redirect Escherichia coli phage scaffolds to target pathogenic Yersinia and Klebsiella bacteria, and conversely, Klebsiella phage scaffolds to target E. coli by modular swapping of phage tail components. The synthetic phages achieved efficient killing of their new target bacteria and were used to selectively remove bacteria from multi-species bacterial communities with cocktails based on common viral scaffolds. We envision this approach accelerating phage biology studies and enabling new technologies for bacterial population editing.

Strains IJ284 Klebsiella sp. 390, IJ1668 K-12 hybrid; K1 capsule, IJ612 S. typhimurium LT2, K1E, K1F, K1-5, SP6, and K11 were kindly provided by Ian Molineux (University of Texas at Austin). LUZ19 was kindly provided by Rob Lavigne (KU Leuven). Y. pseudotuberculosis IP2666 and YPIII were kindly provided by Joan Mecsas (Tufts University). We thank Oliver Purcell and Jennifer Henry for critically reading the manuscript. This work was supported by grants from the Defense Threat Reduction Agency (HDTRA1-14-1-0007), the NIH (1DP2OD008435, 1P50GM098792, and 1R01EB017755), and the U.S. Army Research Laboratory/Army Research Office via the Institute for Soldier Nanotechnologies (under contract number W911NF-13-D-0001). H.A. was supported by fellowships from the Japan Society for the Promotion of Science and the Naito Foundation. D.P.P. was supported by the Portuguese Foundation for Science and Technology (SFRH/BD/76440/2011).