PhD Position in Bioscience Engineering

University of Antwerp


Department: Department of Bioscience Engineering
Regime Full-time

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The University of Antwerp is a dynamic, forward-thinking, European university. We offer an innovative academic education to more than 20,000 students, conduct pioneering scientific research and play an important service-providing role in society. We are one of the largest, most international and most innovative employers in the region. With more than 6,000 employees from 100 different countries, we are helping to build tomorrow's world every day. Through top scientific research, we push back boundaries and set a course for the future – a future that you can help to shape.

The Lebeer Lab at the Department of Bioscience Engineering in the Faculty of Science is looking for a full-time (100%) PhD student to study the ecology and evolution of the female microbiome through bioinformatic analysis of DNA and RNA sequencing data.

The Lebeer Lab performs cutting edge research on Lactic Acid Bacteria and their habitats, including the human microbiome (with a special focus on the vaginal microbiome) but also vegetable fermentations, insects and plants. Prof. Sarah Lebeer holds a prestigious ERC Starting Grant on the ecology, evolution and beneficial potential of lactobacilli. In 2020, the group launched the Isala citizen science project on the female microbiome, with more than 3,000 participants.

The human vaginal microbiome is crucial for women’s health and reproduction, but it is understudied compared to other human microbial environments such as the gut. Humans have a unique vaginal flora compared to other primate and mammal species, but it is currently unclear to what extent, and how, the typical human vaginal bacteria adapted to this environment on the evolutionary timescale. On the ecological timescale, within the lifetime of a woman, we do not yet know where vaginal bacteria are obtained and how transient they are in the vaginal community. Through the Isala project and its many spinoff projects, the Lebeer Lab generates large amounts of amplicon, genome, metagenome and (meta)transcriptiome sequencing data. The goal of this PhD project is to mine this in-house sequencing data, supplemented with publicly available datasets, to gain insights into the structure, dynamics and evolutionary history of the human female microbiome. This PhD focuses on fundamental research questions, but a better understanding of these topics will lead to treatment strategies and/or lifestyle recommendations that will improve women’s health and pregnancy outcomes.


  • You will work actively on the preparation and defense of a PhD thesis on the topic of the ecology and evolution of female microbiome. Your own research interests and ideas surrounding this topic are welcomed and encouraged.
  • Your research will mainly entail the development and application of computational pipelines for DNA and RNA sequencing data analysis.
  • You will publish scientific articles on your research.
  • You will present your work at national and international workshops and conferences.
  • You will apply for an FWO PhD fellowship on the topic of the female microbiome, again with considerable room for your own interests and ideas. There is in-house funding available so failing to obtain such a fellowship poses no problem.
  • You will carry out a limited number of teaching and research support tasks for the department of Bioscience Engineering.


  • You hold a Master degree in bioinformatics or you hold a Master degree in biology, bioscience engineering, biochemistry or biomedical sciences and you have experience with bioinformatics. Last year Master students can also apply.
  • You can work fluently with Linux and Bash.
  • You can code in Python and/or R.
  • You have a solid understanding of molecular biology and microbiology.
  • You are interested in microbial ecology and evolution and in the human microbiome.
  • You are interested in learning how to analyze microbial genome, metagenome and (meta)transcriptome sequencing data through various techniques, including (meta)genome assembly, read mapping to reference genomes and phylogenetic analysis.
  • Excellent study results are considered a plus.
  • You have good oral and written knowledge of English.
  • Your teaching competences are in line with the University of Antwerp’s educational vision.
  • Your research qualities are in line with the faculty and university research policies.
  • You act with attention to quality, integrity, creativity and cooperation.

What we offer

  • We offer a doctoral scholarship for a period of two years. Following a positive evaluation, the scholarship can be renewed once for another two-year period.
  • We offer the opportunity for solid bioinformatics and microbiology training, with coaching by experienced postdocs in (microbial) bioinformatics.
  • The planned start date is 9 October 2023 or as soon as possible after that date.
  • Your monthly scholarship amount is calculated according to the scholarship amounts for doctoral scholarship holders on the pay scales for Contract Research Staff (Dutch: Bijzonder Academisch Personeel, BAP).
  • You will receive ecocheques, Internet-connectivity allowance and a bicycle allowance or a full reimbursement of public transport costs for commuting.
  • You will do most of your work at Campus Groenenborger in a dynamic and stimulating working environment.
  • Find out more about working at the University of Antwerp here.

Want to apply?

  • You can apply for this vacancy through the University of Antwerp’s online job application platform up to and including 21 August 2023 (by midnight Brussels time). Click on the 'Apply' button, complete the online application form and be sure to include the following attachments: (1) a motivation letter, (2) your CV and (3) contact info for one or two references.
  • The selection committee will review all of the applications as soon as possible after the application deadline. As soon as a decision has been made, we will inform you about the next steps in the selection procedure. The interviews will take place on 6 September 2023.
  • If you have any questions about the online application form, please check the frequently asked questions or send an email to If you have any questions about the job itself, please contact dr. Stijn Wittouck, senior bioinformatician at the Lebeer Lab, (

The University of Antwerp received the European Commission’s HR Excellence in Research Award for its HR policy. We are a sustainable, family-friendly organisation which invests in its employees’ growth. We encourage diversity and attach great importance to an inclusive working environment and equal opportunities, regardless of gender identity, disability, race, ethnicity, religion or belief, sexual orientation or age. We encourage people from diverse backgrounds and with diverse characteristics to apply.

In your application, please refer to