Post-Doctoral Researcher, APC Microbiome Ireland

University College Cork
February 16, 2024
Offerd Salary:€42,781 - €49,177
Working address:N/A
Contract Type:Other
Working Time:Negotigation
Working type:N/A
Ref info:N/A
Post-Doctoral Researcher, APC Microbiome Ireland

2 Years, Fixed-Term, Whole-time Post

Position Summary

We are looking for a talented and enthusiastic Post-Doctoral Researcher to join an ERC-funded research project investigating the role of bacteriophages in horizontal gene transfer in the human gut microbiome.

The PHAGENET focuses on the role of phage transduction in the rapid microbial evolution in the human gut, dissemination of beneficial and detrimental (e.g. antibiotic resistance) genetic determinants, as well as its wider implications for microbial ecology. The research will involve an array of approaches, including long-read high-throughput sequencing, faecal chemostat models, random transposon insertion libraries in gut bacteria and animal colonisation models.

At the core of this project is an ex vivo anaerobic faecal microbial chemostat model, designed to enable exchange of virus-like particles (VLPs) between two spatially segregated microbial communities, allowing to monitor VLP- mediated gene flow and transfer of phage communities between individual microbiomes. Analysis of phage transduction and other modes of HGT in the complex community will be performed through tracking of transposon-labelled mobilised bacterial DNA, isolation and sequencing of individual bacterial cultures (strict anaerobes), shotgun metagenomics, long-read sequencing of virus-like particle (VLP)-associated DNA.

The Post-Doctoral Researcher's main focus will be either on wet lab or dry lab aspects of this work (or a combination of both), depending on their existing skill set, professional growth ambitions and personal scientific interests. A skilled research assistant will be available to help with faecal chemostat experiments. The wet lab role requires excellent skills in classical bacteriology and strict anaerobe culture, bacteriophage isolation techniques. Knowledge of transposon mutagenesis, microbial bioreactors, NGS library preparation and sequencing techniques, are highly desirable. The dry lab role will require core skills in biostatistics and multivariate statistical learning; good command of bash, R and/or Python environments; metagenomics data analysis, including reference mapping and de novo assembly or short and long reads (Illumina, Oxford Nanopore); binning, annotation and classification of phage and bacterial genomes and MAGs; SNP and SV calling; identification of HGT events. Deep understanding of phage biology, with a special focus on phage transduction, gene-transfer agents and other phage-like elements and VLPs, is a requirement for both roles.

The project is hosted within the APC Microbiome Ireland Gut Phageomics lab, an established research hub for bacteriophage biology. APC Microbiome Ireland was formed in 2003 and since then it has established itself as one of the leading global centres in the microbiome research. The centre has made several landmark discoveries and has published over 1,000 research articles in peer- reviewed journals, generating many journal covers and associated editorials. The APC is a lively trans-disciplinary environment with clinicians, clinician- scientists and basic scientists from diverse backgrounds working in teams, sharing ideas and resources.

This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 101001684).

For more information, we encourage prospective candidates to contact Principal Investigator Prof. Andrey Shkoporov at [email protected]

UCC is an accredited research organisation and as such can form hosting agreements with third country nationals (and non-EEA nationals) for the purpose of conducting research in the University.

Project Title: PHAGENET: PHAge GEnetic NETworking in the microbiome

Post Duration: 2 years

Salary: €42,781 - €49,177 p.a. (IUA PD1 Salary Scale)

For an information package including further details of the post see https: //

Informal enquiries can be made in confidence to Prof. Andrey Shkoporov, School of Microbiology & APC Microbiome Ireland, University College Cork; Tel: + 353 (0) 21 490 1771; Email: [email protected]

Applications must be submitted online via the University College Cork vacancy portal (https: // Queries relating to the online application process should be referred to [email protected], quoting the job-title and project name.

Candidates should apply, in confidence, before 12 noon (Irish Local Time) on Friday, 16th February 2024.

No late applications will be accepted.

Please note that an appointment to posts advertised will be dependent on University approval, together with the terms of the employment control framework for the higher education sector.


Contact Person : Andrey Shkoporov Contact Email : [email protected] Job ID : 074031 Contact Number : Close Date : 16-Feb-2024 12:00

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