(BBSRC DTP Studentship) Profiling the biodiversity and host-specificity of the virome, the viral component of the microbiome

Principal Supervisor: Professor David Robertson

Funding

Funding available for eligible UK/EU applicants.

Description

The use of bacteriophages (viruses that infect and replicate in bacteria) as anti-bacterial therapeutics will be increasingly important for the treatment of animal, plant and human infections as the problem of antibiotic resistance worsens. The property of bacteriophages (phages) that is most valuable is the specificity of the viral-host relationship. Unlike the broad-spectrum nature of antibiotics, a phage should target a specific bacteria species. However, what are the limits of this specificity? What is the impact of viruses on the diversity and make-up of the microbiome? In this project we propose to study the host-specificity of phages for their bacterial hosts, the impact of phage presence on microbiome community structure, and bacterial population variation. To do this we will use species co-occurrence approaches from the ecological literature applied to published metagenome data sets from different samples, detection of viruses integrated into bacterial genomes (prophages) and fragments of phages associated with the bacterial defence systems CRISPR as signals for viral-host interactions. Combined with the extensive knowledge of bacterial-phage interactions in the primary literature the aim will be to infer the host range of individual phages, coevolutionary relationships and identify host genes (for example, receptors) that are predictive of infectiousness and potential for host-switching.

http://www.manchester.ac.uk/research/david.robertson

http://www.manchester.ac.uk/research/tucker.gilman

http://www.manchester.ac.uk/research/james.mcinerney

Related Publications

  • Faust K, Raes J (2012) Microbial interactions: from networks to models. Nat Rev Microbiol.10:538-50.
  • Flores CO, Meyer JR, Valverde S, Farr L, Weitz JS (2011) Statistical structure of host-phage interactions. PNAS 108:E288-97.
  • Paterson S, Vogwill T, Buckling A, Benmayor R, Spiers AJ, Thomson NR, Quail M, Smith F, Walker D, Libberton B, Fenton A, Hall N, Brockhurst MA (2010) Antagonistic coevolution accelerates molecular evolution. Nature 464:275-8.
  • Roux S, Hallam SJ, Woyke T, Sullivan MB (2015) Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife 4:e08490.
  • Stern A, Mick E, Tirosh I, Sagy O, Sorek R (2012) CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Res. 22:1985-94.

Subject Areas

  • Bioinformatics
  • Biotechnology
  • Genetics
  • Microbiology
  • Molecular Biology
  • Plant Sciences

How to Apply

This project is to be funded under the BBSRC Doctoral Training Programme.   Projects under this scheme are competitively funded; ie there are more projects advertised than are available.  If you are interested in this project, please make direct contact with the Principal Supervisor to arrange to discuss the project further as soon as possible.  You MUST also submit an online application form, full details on how to apply can be found on the BBSRC DTP website http://www.dtpstudentships.manchester.ac.uk/