Targeted phage metagenomics

Qualification: PhD

Department: Genetics

Application deadline: 31 May 2021

Start date: 27 September 2021

Overview

Supervisors

Dr Ed Galyov and Dr Andrew Millard

Project description:

Scientific rationale:

Bacteriophages are the most abundant biological entities on the planet with 1031 in the biosphere. They drive the evolution of their bacterial hosts by mediating horizontal gene transfer, facilitating the spread of antimicrobial resistance and virulence genes. Despite being abundant, we have only begun to understand their diversity through culture-independent methods (eg viral metagenomics). Although viral metagenomics has expanded our understanding of phage diversity, critically it does not link the phage with host that it can infect. The range of hosts a phage can infect is traditionally based on the use of plaque assays that allows the visualisation of plaque, should the infection results in a productive infection. However, there are many issues with this method. First, if the phage is temperate in nature, it will not produce plaques. Additionally, the phage may be able to attach and inject its DNA (also transferred genes) but not be able to actively replicate due to host anti-phage systems. Linking phage diversity to hosts and identifying the range of host phage can transfer genetic material between is essential to understand the role of phages in host evolution. Furthermore, with growing use of phage therapy and use of phage as delivery vectors identifying the full range of hosts will be essential for the success of such approaches. This work will build on the preliminary data we have for the production of mini-cells of E. coli MG1655 and subsequent infection with phages. Mini-cells are "mini" bacterial cells that contain no chromosomal DNA but crucially contain membrane receptors for phage attachment. We hypothesise that it is possible to exploit these cells to develop a novel methodology for assessing host-specific viromes. This will be achieved by infecting mini-cells with phages from an environment, then separating non-attached phages, isolating DNA from phages infecting mini-cells, enabling, combined with metagenomics, the identification of all phages capable of infection of that particular host. This will directly link phages to a host, revolutionising the field of phage metagenomics.

Proposed work:
Objective 1: Expand the production of mini-cells beyond E. coli with the first target being Vibrio natriegens 
Objective 2:  Test and optimise with a defined cocktail of phages, with known host ranges, the limits of detection of mini-cells combined with metagenomics to identify host specific interactions. 
Objective 3. Apply the use of mini-cells to produce host specific metagenomes from animals slurries (E. coli) and aquaculture (Vibrio)
Objective 4. Apply the use of mini-cells to identify the extent different phages are capable of mediated horizontal gene transfer 

Potential Impact: Unlike traditional viral metagenomics, the use of mini-cells offers the crucial ability to directly link phages with the hosts they can infect. Furthermore, it provides a high-throughput way to identify the extent of phages can mediated the transfer of genes. 

Primary methods of the project: This project will use traditional microbiology/phage biology methods (bacterial cultivation and genetic modification, collection of environmental phage samples, phage concentration, assessment of phage-bacteria interactions, etc.); synthetic biology for production of mini-cells; and metagenomic sequencing and bio-informatic analysis of sequence data.

 

Funding

Funding

The Studentship provides: 

  • 3 Years of stipend at UKRI rates
  • 3 Years tuition fees at UK rates

Entry requirements

Entry requirements

UK Bachelor Degree with at least 2:1 in a relevant subject or overseas equivalent.

The University of Leicester English language requirements apply where applicable.

Informal enquiries

Informal enquiries

Project enquiries to Dr Ed Galyov eg98@le.ac.uk

Application enquiries to pgradmissions@le.ac.uk

How to apply

How to apply

To submit your application, please use the Apply button at the bottom of the page and select September 2021 from the dropdown menu.

With your application, please include:

  • CV
  • Personal statement explaining your interest in the project, your experience and why we should consider you
  • Degree Certificates and Transcripts of study already completed and if possible transcript to date of study currently being undertaken
  • Evidence of English language proficiency if applicable
  • In the reference section please enter the contact details of your two academic referees in the boxes provided or upload letters of reference if already available
  • In the funding section please specify that you wish to be considered for the GGB Galyov 2021 studentship
  • In the research proposal section please provide the names of the project supervisors and project title (a research proposal is not required)

Eligibility

Eligibility

This PhD studentship is available to UK/EU applicants only.