PhD position: Bacterial RNA biology in the gut microbiota

Code: 49/2018



The research group “Host-Pathogen-Microbiota Interaction” (HOPI) of Jun. Prof. Alex Westermann at the Helmholtz Institute for RNA-based infection research (HIRI) in Würzburg (Germany) is offering a PhD position: “Bacterial RNA biology in the gut microbiota”.


The HIRI is recruiting a doctoral researcher to identify and characterize noncoding RNAs and RNA-binding proteins (RBPs) in selected bacterial members of the mammalian gut microbiota. The successful applicant will work with experienced scientists and bioinformaticians to transfer various RNA sequencing-based techniques – already established at the HIRI – to the respective commensal bacterial species. The project will rely on microbiological techniques, RNA-seq data generation, interpretation and validation, and the mechanistic characterization of the resulting RNA and RBP candidates using a variety of biochemical approaches.

The successful applicant will work in the dynamic environment of the HIRI in Würzburg, which is part of the Helmholtz Centre for Infection Research ( The selected doctoral researcher will further be embedded within the highly successful structured doctoral training program of the Graduate School Life Sciences (GSLS) Würzburg (

Further reading:

  • Westermann et al. (2016) Nature 529:496-501.
  • Westermann & Barquist et al. (2017) Plos Pathog 13(2):e1006033.
  • Hör, Gorski, Vogel (2018) Mol Cell S1097-2765(17)30980-2.



  • Master’s Degree/Diploma in molecular biology, microbiology, immunology, biotechnology, bioinformatics, or a related field 
  • Basic practical molecular biological, biochemical and/or microbiological skills 
  • Previous experience in infection biology, bacteriology, or RNA biology
  • Strong written and spoken English language communication skills 
  • Ability to work independently and as part of an international team 
  • A strong desire to do research, enthusiastic, creative, and highly self-motivated

Desired (non-essential) background:

  • Previous experience working with large-scale biological data sets, particularly RNA-seq
  • Familiarity with the microbiome
  • Knowledge of a scripting language (Python, Perl, etc.) and R


HIRI Würzburg

Research Group

The Handicapped

Qualified applicants with a disability will be given preference.

Starting date


Contract time limit

Initial term 1 year, with the possibility of an extension of additional 2 years

Probation period

6 months


alike TVöD E13 (50%) with the possibility of an additional payment of 10%

Published on


Applications accepted until  29.07.2018

Applicants are required to complete the online application form here: (Please refer to the job number 49/2018.

For more details regarding the PhD project, please contact Jun. Prof. Alex Westermann via e-mail:

The Helmholtz Institute for RNA-based Infection Research (HIRI) has been established in May 2017 as joint venture between the Helmholtz Centre for Infection Research (HZI) and the Julius Maximilian University of Würzburg (JMU). Located on the Würzburg medical campus, it is the first research institution worldwide to exclusively address the role of ribonucleic acids (RNAs) in infection processes. Based on these findings, the HIRI will pioneer an integrative approach to exploit the vast potential of RNAs as a diagnostic molecule, target and drug for new strategies to combat infectious diseases.

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HZI International Graduate School

The HZI International Graduate School for Infection Research (GS-FIRE) provides an innovative structured PhD programme within the field of Infection Research.

PhD programme “Epidemiology”

The PhD programme “Epidemiology” is a three-year doctoral programme in the area of epidemiological research and is coordinated by the Department of Epidemiology of the HZI.

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