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Bioinformatics analyses of microbial communities and their genetic contents to understand the transmission dynamics and selection of antimicrobial resistance


   Department of Biomedical Sciences

  ,  Applications accepted all year round  Self-Funded PhD Students Only

About the Project

Project Overview

Antimicrobial Resistance (AMR) is one of the topics that we cannot ignore. Bacterial infections unsuccessfully treated due to AMR claim at least 700 000 lives per year worldwide and are projected to be associated with the deaths of 10 million people per year by 2050. The evidence suggests that AMR in human bacterial pathogens originates from several bacterial sources, indicating that the genetic material of all bacteria can be considered as a single global gene pool which most, if not all, bacteria can exploit for genes necessary for their survival. When it comes to AMR, plasmids play one of the most dominant roles as carriers of resistance genes and for their dissemination. However, understanding how the resistance “moves” around is extremely challenging and requires a wholistic approach which calls for extensively analysing and investigating a huge dataset. 

This project will develop novel bioinformatic strategies to integrate and analyse a large collection of Next Generation Sequencing data (shotgun metagenomes) obtained from hospitals and the environments to investigate the microbial diversity of AMR bacteria and plasmids, and the dynamics of transmission as well as selection of resistance at a multi-dimensional scale. This will enable us to better understand and evaluate preventive and intervening measures to slow the spread of antibiotic resistance genes and bacteria and keep our antibiotic medicines useful.  

 

Gweon Lab – Molecular Ecology, Genomics and Bioinformatics: 

We aspire to better understand some of the most challenging questions in the abundance, diversity, activity, and interactions of microbes in a wide range of ecosystems using advanced techniques and technologies. We are fully equipped for state-of-the-art molecular biology, genomics and bioinformatics research and have the capacity of accommodating high-throughput molecular biology research as well processing Big Data using our High-Performance Computing servers dedicated for multi-omics analyses. Due to the multidisciplinary nature of the research being undertaken by the group, we welcome students from a range of backgrounds who are ready for new challenges.  

 

School of Biological Sciences, University of Reading: 

The University of Reading, located west of London, England, provides world-class research education programs. The University’s main Whiteknights Campus is set in 130 hectares of beautiful parkland, a 30-minute train ride to central London and 40 minutes from London Heathrow airport.    

Our School of Biological Sciences conducts high-impact research, tackling current global challenges faced by society and the planet.  Our research ranges from understanding and improving human health and combating disease, through to understanding evolutionary processes and uncovering new ways to protect the natural world.  In 2020, we moved into a stunning new ~£60 million Health & Life Sciences building. This state-of-the-art facility is purpose-built for science research and teaching.  It houses the Cole Museum of Zoology, a café and social spaces. 

In the School of Biological Sciences, you will be joining a vibrant community of ~180 PhD students representing ~40 nationalities. Our students publish in high-impact journals, present at international conferences, and organise a range of exciting outreach and public engagement activities.  

During your PhD at the University of Reading, you will expand your research knowledge and skills, receiving supervision in one-to-one and small group sessions. You will have access to cutting-edge technology and learn the latest research techniques.  We also provide dedicated training in important transferable skills that will support your career aspirations. If English is not your first language, the University's excellent International Study and Language Institute will help you develop your academic English skills. 

The University of Reading is a welcoming community for people of all faiths and cultures.  We are committed to a healthy work-life balance and will work to ensure that you are supported personally and academically.  

Eligibility: 

Applicants should have a good degree (minimum of a UK Upper Second (2:1) undergraduate degree or equivalent) in science or a related discipline (including mathematics and physics).  Applicants will also need to meet the University’s English Language requirements. We offer pre-sessional courses that can help with meeting these requirements. 

 

How to apply: 

Submit an application for a PhD in Biological Sciences at http://www.reading.ac.uk/pgapply

 

Further information: 

http://www.reading.ac.uk/biologicalsciences/SchoolofBiologicalSciences/PhD/sbs-phd.aspx 

 

Enquiries: 

Dr Soon Gweon, email: , homepage: https://hsgweon.github.io/ 

Please see Dr Soon Gweon's profile:

https://www.reading.ac.uk/biologicalsciences/about/staff/h-s-gweon.aspx 

 


Funding Notes

We welcome applications from self-funded students worldwide for this project.
If you are applying to an international funding scheme, we encourage you to get in contact as we may be able to support you in your application.

References

Gweon, H. S., Shaw, L. P., Swann, J., De Maio, N., AbuOun, M., Niehus, R., Hubbard, A. T. M., Bowes, M. J., Bailey, M. J., Peto, T. E. A., Hoosdally, S. J., Walker, A. S., Sebra, R. P., Crook, D. W., Anjum, M. F., Read, D. S., Stoesser, N. and REHAB Consortium, (2019) The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples. Environmental Microbiome, 14 (1). 7. ISSN 2524-6372

Matlock, W., Chau, K. K., AbuOun, M., Stubberfield, E., Barker, L., Kavanagh, J., Pickford, H., Gilson, D., Smith, R. P., Gweon, H. S., Hoosdally, S. J., Swann, J., Sebra, R., Bailey, M. J., Peto, T. E. A., Crook, D. W., Anjum, M. F., Read, D. S., Walker, A. S., Stoesser, N. and Shaw, L. P. (2020) Genomic network analysis of environmental and livestock F-type plasmid populations. The ISME Journal. ISSN 1751-7370

Kotay, S. M., Parikh, H. I., Barry, K., Gweon, H. S., Guilford, W., Carroll, J. and Mathers, A. J. (2020) Nutrients influence the dynamics of Klebsiella pneumoniae carbapenemase producing enterobacterales in transplanted hospital sinks. Water Research, 176. 115707. ISSN 0043-1354

Constantinides, B., Chau, K. K., Quan, T. P., Rodger, G., Andersson, M. I., Jeffery, K., Lipworth, S., Gweon, H. S., Peniket, A., Pike, G., Millo, J., Byukusenge, M., Holdaway, M., Gibbons, C., Mathers, A. J., Crook, D. W., Peto, T. E. A., Walker, A. S. and Stoesser, N. (2020) Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients. Microbial Genomics, 6 (7). ISSN 2057-5858

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