PhD position: Bacterial RNA biology in the gut microbiota

Code: 64/2018



The research group “Host-Pathogen-Microbiota Interaction” (HOPI) of Jun. Prof. Alexander J. 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 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. (

Project description:

The HIRI is recruiting a doctoral student to identify and characterize noncoding RNAs and RNA-binding proteins (RBPs) in anaerobic bacterial members of the mammalian gut microbiota. The project will rely on microbiological and cell-culture techniques, CRISPR interference screening, RNA-seq approaches, and the mechanistic characterization of the resulting RNA and RBP candidates using bacterial genetics and 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 applicant 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 and/or CRISPRi data
  • Familiarity with the microbiome
  • Knowledge of a scripting language (Python, Perl, etc.) and R 


HIRI Würzburg

The Handicapped

Qualified applicants with a disability will be given preference.

Special preference toward women


Starting date

November 15, 2018

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%

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Applications accepted until  14.10.2018

Applicants are required to complete the online application form here: (Please refer to the job number 64/2018)

For more details regarding the PhD project, please contact Jun. Prof. Alexander J. Westermann via   E-Mail: 

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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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