A protocol to study bacteriophage adaptation to new hosts

• Published in: STAR protocols Vol. 2; no. 3; p. 100784
• Main Authors: Luzon-Hidalgo, Raquel, Risso, Valeria A., Delgado, Asuncion, Ibarra-Molero, Beatriz, Sanchez-Ruiz, Jose M.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 17.09.2021; Elsevier
• Subjects: Adaptation, Biological - genetics; Bacteriophage T7 - genetics; Bacteriophages - genetics; Biophysics; Biotechnology and bioengineering; Escherichia coli - genetics; Evolutionary biology; Genome, Viral - genetics; High-Throughput Nucleotide Sequencing - methods; Host-Pathogen Interactions - genetics; Microbiology; Model organisms; Molecular biology; Protocol; Sequence Analysis, DNA; Virology - methods; Biophysics; Model organisms; Microbiology; Biotechnology and bioengineering; Evolutionary biology; Molecular biology
• ISSN: 2666-1667; 2666-1667
• DOI: 10.1016/j.xpro.2021.100784

A general protocol for the experimental assessment of bacteriophage adaptation to new hosts is described. We use as a model system the lytic phage T7 and an engineered E. coli strain modified to hamper the recruitment of a known proviral factor. Our protocol includes steps of phage amplification, plaque and liquid lysis assays, and DNA extraction for next-generation sequencing of the viral genome over several rounds of laboratory evolution thus allowing the investigation of the sequence determinants of viral adaptation. For complete information on the generation and use of this protocol, please refer to Luzon-Hidalgo et al. (2021). [Display omitted] •Protocol for experimental characterization of phage adaptation to new hosts•DNA extraction for NGS of viral genome to unwind the molecular basis of adaptation•Potential application in the development of anti-microbial phage therapies A general protocol for the experimental assessment of bacteriophage adaptation to new hosts is described. We use as a model system the lytic phage T7 and an engineered E. coli strain modified to hamper the recruitment of a known proviral factor. Our protocol includes steps of phage amplification, plaque and liquid lysis assays, and DNA extraction for next-generation sequencing of the viral genome over several rounds of laboratory evolution thus allowing the investigation of the sequence determinants of viral adaptation.