Biophysical modelling of antibiotic efflux in bacterial biofilms

Doctoral Researcher Project No: 2389/2022

In this PhD project, we will use mathematical and computational modelling to disentangle the relationship between efflux, persistence and tolerance in spatially structured bacterial biofilms. The project will combine coarse-grained modelling (deme-based models) with more individual-based biofilm modelling. This position is part of the SPP 2389 project ‘Antibiotic tolerance of biofilms emerging from multicellular effects of antibiotic efflux’, in collaboration with the group of Dr. Frank Schreiber at the Federal Institute for Materials Research and Testing (Bundesanstalt für Materialforschung und -prüfung) in Berlin.

Supervisor: Prof. Dr. Rosalind Allen

Tracking the dynamics of interacting microbial populations

Doctoral Researcher Project No: 285/2022

This project focuses on microbial interactions that occur in when one microbial species produces a chemical effector (e.g. a toxin), while a second species produces an enzyme that modifies the effector (e.g. activates or deactivates it). Enzymatic modification of a chemical effector is a common theme in ecological interactions, which has emerged from several other ChemBioSys projects.

The project is part of the DFG-funded Collaborative Research Center 1127 "ChemBioSys – Chemical Mediators in Complex Biosystems"

Supervisor: Prof. Dr. Rosalind Allen

Further job openings in the thematic area

Doctoral Researcher Project : Genomics of Bacteriophage-Host Interactions

The Viral Ecology and Omics Group of Prof. Bas E. Dutilh, studies microbiome functioning and dynamics, in particular the role of viruses across biomes. We combine microbiological and eco/evolutionary experiments with molecular biology, microscopy, (meta‑) genomics, bioinformatics, artificial intelligence, and computational modelling.

Supervisor: Prof. Dr. Bas Dutilh

Please note - applications for this project will not be accepted via the application portal, but can be sent directly to jannick.van.cauwenberghe@uni-jena.de

Identification of universal mediators of microbiome community structure through large scale cross-habitat comparisons

Microverse Postdoctoral Researcher Project No: 03/2022

An exciting new frontier in microbiome research is the rational editing of disbalanced microbial communities. However, the selection of species to be either introduced directly or serve as chassis strains for modifying the structure and function of a dysbiotic microbiome is challenging since many criteria must be fulfilled. In most cases the selection of promising species is based on the ability to cultivate and genetically modify them and their known phenotypic properties, however, their ecological properties are rarely considered. Towards this direction, we plan to develop artificial intelligence workflows using large-scale community sequencing data sets from host, soil, and aquatic environments to shed light on the ecological properties of the different genera and on the potential of using them as global or habitat-specific modifiers of microbial communities. Therefore, the successful candidate is expected to elucidate factors that determine microbial colonization and persistence, as well as, microbial interdependencies within complex communities.

Supervisor: Prof. Gianni Panagiotou

Microbial Ecology/Molecular Microbiology/Biostructural Interactions

Microverse Postdoctoral Researcher Project No: 05/2022

We offer up to three two-year, full-time positions embedded within several research groups in our Cluster of Excellence, e.g., the Papenfort lab, the Stallforth lab, the Hellmich group, in close collaboration with the groups of Kirsten Küsel, Georg Pohnert, Axel Brakhage and Christian Eggeling.  

The project will focus on the interaction of commensal and pathogenic microorganisms with microplastic particles in the environment. Research over the past few years has revealed that microplastic particles can be detected in nearly all habitats (marine, soil, etc.), however, it is frequently unclear if and how microplastic particles affect the composition of microbial consortia and the overall performance of the microbiome. In this project, we aim to understand: a) the molecular factors underlying attachment of microorganisms to microplastic particles, b) the role of extracellular communication molecules for microbial proliferation on microplastic, and c) the impact of microplastic 3D structure and composition on this process

Supervisors: Prof. Dr. Ute Hellmich, Prof. Dr. Kai Papenfort, Prof. Dr. Pierre Stallforth