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EASTBIO: Application of MinION Nanopore sequencing to understand the impact of environmental changes on sentinel indicators of ecosystem health

  • Full or part time
  • Application Deadline
    Sunday, January 05, 2020
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

About This PhD Project

Project Description

We are increasingly aware that human, veterinary and environmental health is intricately linked and farming and food production systems must not only be resilient to environmental changes and threats but the systems themselves must also perform with minimal environmental impact.

This exciting multidisciplinary PhD project takes a “One Health” approach by focussing on sentinel wildlife species that act as indicators of environmental health and resilience. By understanding and monitoring contamination of these sentinels we can more fully understand the impact of pressures such as pollutants and contaminants arising from human activity, including farming, as well as climate change. This in turn provides important information relating to both human and livestock health.

The grey seal (Halichoerus grypus) is an important sentinel species and indicator of coastal marine health. We are investigating the occurrence of bacterial and viral pathogens within grey seal populations as a result of anthropogenic activity (Baily et al. 2015), as well as the incidence of antimicrobial resistance genes. Our research currently focusses on differences between seal colonies in close proximity to large human populations versus remote sites around the north and west coast of Scotland.

Previously, conventional, targeted methods such as laboratory culture and PCR have been used to monitor carriage of bacteria and viruses by sentinel species. In recent years, development of 3rd generation sequencing technologies has enabled enhanced microbe detection due to the ability to sequence long reads. This novel technology can be used to interrogate the presence of bacterial and viral species within environmental samples as well as conduct quantitative metagenomic analysis of the gut microbiome, a key indicator of health.

We propose to apply and assess this technology in addressing three specific areas related to anthropogenic environmental contamination and ecosystem resilience, focussing on coastal grey seal populations within the UK:

Quantitative metagenomic analyses to assess the effects of anthropogenic environmental contamination on the host microbiome and gut health.

Deep sequencing to identify gut bacterial species within grey seals from areas close to human and livestock populations and those distant from them. This analysis will also be integrated with detection of antimicrobial resistance and heavy metal resistance genes to develop and assess pipelines to further understand the origin of these genes and routes of transmission.

Analysis of environmental samples (soil, seabird faeces, water etc.) to further understand transmission routes and the impact of changing climate conditions on disease reservoirs.

Analytical pipelines developed through this multidisciplinary project can then be applied to address the impact of other major global issues, including marine pollution and climate change, on sentinel populations.

The student will be a part of the EASTBIO training programme and will acquire the necessary training in wet lab techniques, sequencing bioinformatics and field work. The supervisory team will provide training and expertise in zoonotic pathogens, antimicrobial resistance and MinION technology (Moredun), sequence analysis and bioinformatic pipelines (Biomathematics and Statistics Scotland) and marine environmental health and ecology (The Sea Mammal Research Unit, University of St Andrews). Candidates with previous knowledge of / experience in bioinformatics are especially encouraged to apply.

Application Procedure:

http://www.eastscotbiodtp.ac.uk/how-apply-0

Please send your completed EASTBIO application form, along with academic transcripts and CV to Moredun Research Institute Human Resources at . Two references should be provided by the deadline using the EASTBIO reference form. Please advise your referees to return the reference form to .

Funding Notes:

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. This opportunity is only open to UK nationals (or EU students who have been resident in the UK for 3+ years immediately prior to the programme start date) due to restrictions imposed by the funding body. Queries on eligibility? Email Human Resources at the Moredun Research Institute at .

Candidates should have (or expect to achieve) a minimum of a First Class Honours degree in a relevant subject. Applicants with a minimum of a 2:1 Honours degree may be considered provided they have a Distinction at Masters level.

We anticipate that an initial interview will be held at the Moredun Research Institute during the week commencing 13th January 2020 with a second EASTBIO interview being held in the week commencing 10th February with awards being made in the following week.

Application deadline is 5th January 2020.

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