Postdoctoral Researcher in Microbiology
University College Cork

Post-Doctoral Researcher, APC Microbiome Ireland

2 Year, Fixed-term, Whole-time Post

Position summary

APC Microbiome Ireland was formed in 2003 and since then it has established itself as one of the leading global centres in gut microbiota research. The centre has made several landmark discoveries and has published over 3,500 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.

We are looking for a talented and enthusiastic Post-Doctoral Researcher to work on a new project investigating the role of bacteriophages in horizontal gene transfer in the human gut microbiome. The project 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. The role requires an exceptional knowledge and skill set spanning anaerobic bacteriology, bacteriophage biology, bacterial genetics and microbiome science.

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).

The ideal candidate for this position should have:

  • Excellent knowledge of anaerobic bacteriology techniques. Experience with isolation and characterisation of strictly anaerobic bacteria.
  • Experience in mouse colonisation experiments, including conventionally-housed and germ free.
  • Experience with isolation, propagation and characterisation of bacteriophages.
  • Experience with in vitro, in vivo, or ex vivo models of phage-bacteria interaction is desirable but not essential.
  • Deep understanding of modern microbiome analysis principles: metagenomics, viromics, culturomics, next-generation sequencing techniques.
  • Proven ability to conduct independent research.
  • Basic bioinformatics literacy (UNIX/Linux systems, shell scripting, R environment, visualisations) is highly desirable.

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: €41,207 - €47,477 p.a. (IUA PD1 Salary Scale)

For an information package including full details of the post

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

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

Candidates should apply, in confidence, before 12 noon (Irish Local Time) on Friday, 31 March 2023. 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.

UCC is committed to creating and fully embracing an inclusive environment where diversity is celebrated. As a University we strive to create a workplace that reflects the diversity of our student population where people from a wide variety of backgrounds learn from one another, share ideas, and work collaboratively. UCC is committed to being an employer that recognises the value of diversity amongst its staff. We encourage applicants to consult our policies at and initiatives at and we welcome applications from everyone, including those who are underrepresented in the protected characteristics set out in our Equal Opportunities & Diversity Policy.


Contact Person : Professor Andrey Shkoporov

Contact Email :

Job ID : 065012

Contact Number :

Close Date : 31-Mar-2023 12:00

If you apply for this position please say you saw it on Bioloxy


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