Molecular Infection Microbiology

Aims

We study how bacterial anti-phage defense systems work together in real time at the single-cell level — mapping the timing, hierarchy, synergy and redundancy between systems such as Zorya, Druantia and Lamassu. These insights inform rational phage therapy and new antimicrobial strategies.

• Watch phage attack and host defenses unfold with high-speed TIRF microscopy and microfluidics.
• Engineer E. coli strains to combine or remove defense modules and track single-cell outcomes.
• Quantify activation order, cross-talk, redundandcy of immune response systems at the singel cell level.
• Develop in-house microfluidic chips and analyses pipelines.

Aims overview

Approach

We use microfluidics and TIRF/live-cell imaging, together with engineered phages, fluorescent reporters, quantitative assays, and custom Python image-analysis pipelines, to map how anti-phage defenses coordinate at single-cell resolution.

• Microfluidics: for long-term time-lapse imaging at single-cell resolution.
• TIRF & live-cell imaging to resolve membrane complexes and subcellular localization of defense systems.
• Engineering phages: genetically modifying phages to track absorbtion or DNA-injection.
• Fluorescent reporters: constructing bacterial strains with transcriptional & translational fluorescence reporters.
• Quantitative assays: Plaque-, and single-cell survival/growth assays.

Tool development

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Lab tour

Mother machine microfluidics

Open positions

We invite applications from students interested in thesis projects in microbiology or microscopy data evaluation. Please contact Philipp Popp with a brief statement of interest and your CV. To assess your motivation, we ask that you include either a short project idea or a description of the methods and approaches you are particularly keen to pursue.