PhD Candidate - Department of Biotechnology

WorkplaceFlemish Region, Ghent, Belgium
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Job description

Short Job Description: PhD position at the interface of gut microbial ecology/immunology at the Center for Microbial Ecology and Technology (CMET, UGent) in the Microbes-4-Immunity project aiming to gain a function-targeted view of host microbiota interactions in health and chronic inflammation Research context: The high incidence of chronic inflammatory and auto-immune disorders, associated with a Western lifestyle, is correlated with the microbiome. Current meta-omics approaches, however, fail to identify the functionally active immunoregulatory microbiota. The interdisciplinary Microbes-4-Immunity project, therefore, aims to generate new insights in microbe-host interactions modulating immunodevelopment and immune homeostasis through a unique combination of single-cell flowcytometric cell sorting, clinical sampling and advanced in vitro and in vivo technologies.
Our offer: You will learn to work with the cutting-edge BONCAT-FACS technology to separate functionally active bacterial subpopulations from health- and disease-associated microbes from animal and human origin. You will further characterize the sorted subpopulations with state-of-the-art culturomics, meta-taxonomics, metagenomics and metabolomics approaches. Finally, you will design and construct miniature microbial ecosystems for biotherapeutic applications and perform mode-of-action studies using the well-validated Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME) in vitro platform. In order to process the generated data you will need to get acquainted with advanced bioinformatics and statistical data integration methods.
Your research will be part of the multidisciplinary Microbes-4-Immunity research project and you will get to interact and cooperate with experts in the field of gastroenterology (Prof. Debby Laukens, Prof. Triana Lobatón), rheumatology (Prof. Filip Van den Bosch, Prof. Koen Venken), in vivo animal research (Prof. Lars Vereecke) and metabolomics (Prof. Lyn Vanhaecke). You will be closely guided by your highly proficient promotors Prof. Tom Van de Wiele and Dr. Chris Callewaert, both affiliated with the Center for Microbial Ecology and Technology (CMET) at the Faculty of Bioscience Engineering, Ghent University. CMET is an international, dynamic, multidisciplinary, intellectually-stimulating and welcoming environment. Working as a PhD candidate in the CMET team will strengthen your scientific communication and reporting skills which you can further improve by frequently giving presentations at (inter)national conferences or attending and holding meetings and (co)-authoring peer reviewed publications in high impact journals. Your professional experience will, furthermore, extend to supervising several bachelor and master thesis students with an academic or technical training background. You will be asked to participate in designing and organizing wet lab practical sessions in the framework of the course ’Interphase processes of host associated microorganisms’.

Your tasks:

  • Validate a viable ’BONCAT-FACS’ workflow for the activity profiling of microbiota from in vivo derived samples (fecal samples and mucosal biopsies of IBD/SpA patients and microbiota samples from multiple mouse gut regions of mice at different ages with different microbiota colonization states: germ-free mice, gnotobiotic mice, specific pathogen free mice and wildling mice)
  • Starting from the sorted active subpopulations: enrich and culture unique gut isolates involved in immunoregulation or disease etiology and progression
  • Apply the optimized viable BONCAT-FACS approach to sort out, culture and characterize tryptophan, mucus and riboflavin metabolizing subpopulations derived from mouse samples and IBD patients
  • Characterize the sorted active subpopulations by Next Generation Sequencing-based taxonomic identification and metagenomic analysis to explore potential pathways that are involved in functions of interest combined with metabolomic analysis of the in vivo samples (mouse models and IBD/SpA patients) to couple functionality with phylogenetic information
  • Integrate the obtained omics-data with host immunological endpoints obtained by the other project partners through programming in a linux/R environment
  • Assemble miniature bacterial ecosystems
  • Perform mode-of-action studies using the Mucosal Simulator of the Human Intestinal Microbial Ecosystem
  • Collaborate with project partners and CMET colleagues
  • Report and communicate your scientific findings to an expert (conferences, publications in scientific journals) and broader non-expert audience (CMET website, science day, Faculty Open Day, own initiatives)

Job profile

We are looking for a highly motivated and talented PhD candidate who is interested to explore the immunoregulatory role of gut microbes in immune homeostasis and chronic inflammation.

Your Competences: knowledge TBD + personality: dependable, kind and good-tempered person with a positive attitude and good communicating skills

How to apply

send in your application letter to by January 31st, together with your CV, a clear motivation of what motivates you to conduct P?hD research on this topic, and include if possible, also a reference letter from previous supervisors.

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In your application, please refer to and reference JobID 5150.