Group and collaboration

Collaboration: Rob Willems & Marc Bonten (Department of Medical Microbiology University Medical Center Utrecht)

PhD student: Paul Stege

PhD defence

Dissertation: Making yourself at home in the intestinal tract – Dynamics of the microbiome, resistome and host-pathogen interactions

Date: 9 November 2022

Project description

This project aims to decipher the processes and molecular mechanisms that contribute to colonization resistance against high density colonization of multidrug resistant (MDR) Enterobacteriaceae and enterococci and the consequences of intestinal outgrowth of MDR Enterobacteriaceae and enterococci on pathogen-host cross-talk when colonization resistance is impaired. This will elucidate the mechanistic foundations, and physiological significance, of beneficial or pathogenic relationships between the gut microbiota and their hosts.

Tasks

1. Metagenomic profiling of the microbial composition of hospitalized patients with and without MDR Enterobacteriaceae and Enterococcus acquisition and high density intestinal colonization.
2. Using metabolomics approaches to define the functional status of the patient-associated microbial ecosystems and bacterial community–host interaction with and without MDR Enterobacteriaceae and Enterococcus acquisition and high density intestinal colonization.
3. Use the data from task-1 and -2 to study in detail inter-bacterial and bacterial-host cross-talk using human intestinal organoids.
4. Study host-specificity of inter-bacterial and bacterial-host cross-talk using different combinations of human and animal-derived strains in in human and animal-derived organoids.