Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing

Abstract

SUMMARY 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 accurately 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 that this approach will accelerate phage-biology studies and enable new technologies for bacterial population editing.

Manipulating Bacterial Communities by in situ Microbiome Engineering

“…By delivering the CRISPR-Cas RNA-guided nuclease system with phages, designated strains can be selectively eliminated based on their genetic content [47]. Furthermore, phage host ranges can be modularly engineered by swapping phage tail components [48]. Altering phage populations represents another avenue for microbiome modulation; exposing the gut microbiome to antibiotics alters its associated virome and ecological networks [49].…”

Genetically Engineered Phages: a Review of Advances over the Last Decade

“…The authors also demonstrated that gene swapping between more distant phage relatives could enable a genetically modified E. coli phage to target Klebsiella bacteria and a genetically modified Klebsiella phage to target E. coli bacteria (Table 1). This work further showed that synthetic phage cocktails composed of phages with the same scaffold but different tail components can be used to target mixed bacterial populations and to selectively remove specific bacterial species from them (85).…”

“…Phage genomes assembled, modified, and propagated in yeast have been isolated and introduced into bacteria to generate functional phage particles (84). This technique has been used to capture and genetically modify the genomes of the coliphages T3 (38,208 bp) and T7 (39,937 bp) (84,85) as well as the Klebsiella phage K11 (41,181 bp) (85). It was further used to capture and archive the genome of fully refactored phage ⌽X174 (6,302 bp) (86).…”

“…Using a yeast-based platform, Ando et al engineered phage genomes to modulate their host ranges (85). Since E. coli phages T7 and T3 share high homology with each other, the authors exchanged the tail fiber gene 17, or fragments thereof, with its counterpart from the other phage, as indicated in Table 1.…”

Emerging Technologies for Gut Microbiome Research

“…Novel methods for selective microbiome modulation, including antibiotic treatment [93], bacteriophage therapy [94-96], dietary supplementation [87], fecal microbiota transplantation [66, 97], and probiotic microbial interventions [88] all provide opportunities to specifically control the composition and/or function of the gut microbial community (Box 3).…”