Job:PhD position in microbial genomics in National University of Ireland, Galway
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7.7 years ago
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Comparative Genomics of Naturalised Soil E. coli Populations - PhD opportunity

We seek highly motivated and able candidates to undertake a PhD project in microbial comparative genomics, to address questions around the naturalisation of Escherichia coli in soil. This project has potential to deliver major advances in our knowledge of the ecology, virulence and diversity of environmentally persistent E. coli, and our understanding of their capacity to adapt to environmental conditions, with practical implications for assessment of human health implications of naturalised populations, and the use of E. coli as an indicator of drinking and recreational water quality. Specific objectives of this project are to determine: (1) whether there is a genomic basis for the remarkable long-term survival of E. coli in maritime temperate soil (2) whether environmentally persistent soil E. coli populations constitute a health risk to human populations (3) if enteric E.coli-specific genomic markers can be constructed. The project will provide valuable multidisciplinary training and research opportunities in computational biology and environmental microbiology. The student will join a successful research group, and lively graduate training communities, and will also receive training in other aspects of scientific work, e.g. result dissemination, writing for publication and conference presentations.

E. coli is the most important faecal indicator for protection of human health from waterborne pathogens. The faecal specificity of E. coli, central to its validity as an indicator, has been questioned. There are widespread reports of long-term persistence and growth of E. coli in soils, and naturalised E. coli populations can survive for upwards of 13 years in maritime temperate soils characteristic of Scotland and Ireland. The disparity between soil and gut environments raises the question of how E. coli populations survive and compete for niche space among highly competitive and diverse populations of indigenous soil microflora, at low temperatures. E. coli growth within soils may provide a reservoir for water contamination, compromising its status as an indicator organism. Understanding ecological characteristics of E. coli in soil is critical for assessment of potential health risks from agricultural activities such as landspreading of manures and slurries.

Applications are invited from graduates with at least a 2.1 BSc or masters in computational biology, microbiology, or a related field. Fluency in English is a requirement. Prior bioinformatics experience would be an advantage. This project will be undertaken in conjunction with the Centre for Human and Animal Pathogens in the Environment, and the Centre for Ecogenomics at the James Hutton Institute (JHI) in Scotland, and builds on successful previous collaborations between the University and the JHI.Supervisors: Dr Fiona Brennan (NUIG), Dr Leighton Prichard (JHI) Dr Florence Abram (NUIG), Dr Nicola Holden (JHI) and Prof Vincent O'Flaherty (NUIG).

This project is available to start immediately. To apply please send a cover letter and a current CV, indicating your research experience and including the names of two referees, to For informal discussion, please contact Dr Fiona Brennan.

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