Description du sujet de thèse

PhD in modelling the dynamics of complex microbial communities

Contexte de travail

- Statistical analysis of microbiota data following exposure to antibiotics and other therapeutic treatments
- Bioinformatic analysis based on genomic data from bacterial communities
- Modelling the dynamics of bacterial communities using ordinary differential equations
- Performing basic bacteriology techniques (mono- and polymicrobial cultures, growth rate measurements, antibiograms, etc.)
- Participating in in vitro experiments in a bacterial community model exposed to invasion by one or more antibiotic-resistant strains.
- Participating in the day-to-day organisation of the laboratory
Analyse bacteriological measurement data (optical density, fluorescence, colony morphology, metagenomics, etc.).
Design and develop theoretical models for the dynamics of natural and laboratory microbial communities.
Simulate communities in silico and analyse their dynamic trends at individual and statistical levels.
Develop analytical techniques to assess the impact of antibiotics on bacterial communities.
Select and adapt protocols for culturing bacterial communities, measuring growth rates, resistance, tolerance and persistence in natural isolates involved in the experiment.
Conduct bacteriological techniques, adapting experimental conditions, to study the colonisation and persistence of antibiotic-resistant strains in different experimental communities.
Participate in training and knowledge exchange with students and other team members.
Theoretical work developed within the groups led by Silvia De Monte (IBENS) and Daniel Amor (LPENS and IAME-INSERM). The candidate will be required to integrate into both groups and divide their work between them. The experimental part will be carried out at IAME-INSERM (Bichat Hospital campus), where Daniel Amor's group has its microbiology laboratory.

Contraintes et risques

Risk related to biological agents
- Risk related to work equipment (hazardous materials, pressurised equipment, vibrating tools, restrictive personal protective equipment (PPE), etc.)
- Risk related to working with display screen equipment (ergonomics, etc.)