PhD Student - Lung Microbial Omics (m/f/d)

 CDD · Thèse  · 36 mois    Bac+5 / Master   Heidelberg University Hospital · Heidelberg (Allemagne)  TVL-E13 65%

 Date de prise de poste : 1 avril 2024


Meta-transcriptomics, metagenomics, respiratory microbiome, interactome, metabolic pathways, R, Python


To understand the mechanisms of priority effects and resistance to microbial colonisation at the play of human lung development (ln parallel in a mouse model in collaboration with Dr Rory Morty from TLRC), we need to unravel the functional basis of interactions within the microbiota of human respiratory tract in infants, children and adults. Our main goal will be to characterize and compare the microbial functions in healthy individuals at different ages versus patients diagnosed with specific respiratory diseases, mainly Cystic fibrosis (CF) or advanced chronic obstructive pulmonary disease (COPD). We hypothesise that the functional core of microbe-microbe interactions is more likely disease-specific and age-specific. To test our hypothesis, in tight collaboration with clinicians at the children's clinic of Heidelberg University Hospital, and the Thoraxklinik, we designed three cohorts of patients with CF (infants, children, and adults) and patients with COPD. Microbiome, shotgun metagenomics and meta-transcriptomics libraries will be prepared in our laboratory with full technical support. The PhD candidate under my supervision will be conducting comparative microbial Omics analyses (metagenomics and meta-transcriptomics) and specific pathogen genome annotations.

Your Tasks

  • Preparation of microbiome, shotgun metagenomics and meta-transcriptomics libraries with technical support
  • Conduction of the microbial Omics analyses (metagenomics and metatranscriptomics)
  • Isolation and sequencing of highly abundant pathogens using a classical genomic approach.
  • Annotation of the metabolic pathways enriched for microbe-microbe interactions.

Your Profil

  • Master’s degree in bioinformatics/computational biology or related fields. MD students with a deep interest in bioinformatics and microbiome science are also welcome
  • Proficiency in R programming is mandatory, and mastering Python language is highly recommended
  • Previous experience in NGS data like metagenomics and transcriptomics analyses would be highly appreciated
  • A good understanding of the multivariate statistical methods for multi-omics data analysis
  • Previous experience with containers (NextFlow or Singularity), package managers (conda, mamba), and basic knowledge of HPC computing, all are appreciated but not mandatory

We offer

  • Collectively agreed remuneration, attractive company pension scheme (VBL)
  • 30 days vacation
  • Sustainable travel: job ticket
  • Family-friendly working environment: cooperative arrangements for childcare, subsidy for child vacation care, advice for employees with relatives in need of care
  • A Wide range of health, prevention and sports offers


Procédure : Send your CV, a cover letter, a summary of your research experience, and the names of two references Applications will be accepted until March 22nd direct online

Date limite : 22 mars 2024


Bachar Cheaib

Offre publiée le 2 février 2024, affichage jusqu'au 21 mai 2024