Mots-Clés

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

Description

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.

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