Single-cell dynamics of bacterial immunity

Bacteria are under constant attack by phages and defend themselves with a remarkable diversity of immune systems. Most species carry several of them, often clustered in defence islands. How these modules are coordinated in time and space, and how they are embedded in the wider physiology of the cell, remains largely unknown.

Defence in concert

Defence systems differ in how they sense infection, where they localise in the cell and when they act, and some confer protection only in combination. The figure maps the systems we study within a single cell, together with current mechanistic knowledge and the open questions we address.

We follow defence in single living cells and connect what we see to the structures of the defence complexes.

1. 1

   Engineer

   Reporter fusion in time-lapse microscopy over two hours.

   We combine or remove defence systems in E. coli, build fluorescent reporters and label phages to follow infection dynamics.

   Delgadillo-Guevara et al. 2024, J Biol Eng

2. 2

   Watch

   Animation: labelled phages reach cells in a mother machine (with Dietrich Kohlheyer, FZ Jülich). Right: real channels with labelled phages.

   Microfluidic mother machines keep thousands of single cells under constant conditions while phages arrive. Live-cell and TIRF microscopy show where and when each defence system acts.

3. 3

   Resolve

   ZorA₅B₂ (PDB 8QYD) between the inner membrane and the peptidoglycan.

   We aim to unravel the mechanistic details of anti-phage defence systems: with structural biologists we determine the architecture of defence complexes and test proposed mechanisms in living cells.

   Hu, Popp et al. 2025, Nature · Himpich et al. 2026, Cell Reports

4. 4

   Quantify

   BactoMate: segmentation, foci, cell outlines and tracking.

   BactoMate, our open-source platform, turns microscopy into single-cell data: segmentation, foci, tracking and lineages, in one workflow.

   Preprint · GitHub · Tutorials

• Oct 2026PeopleWelcome, Nikos MoustakasNikos joins the lab as a PhD student on the Einstein BacDefiant project.
• Jan 2026GrantBacDefiant receives fundingEinstein Foundation Berlin funds BacDefiant with €1.4M over four years.

• Nature 2025Structure and mechanism of the Zorya anti-phage defence systemZorAB is a 5:2 proton-driven rotary motor with a ~70 nm cytoplasmic tail that recruits nuclease effectors after phage sensing.Hu, Popp et al.
• Cell Reports 2026A compact Druantia defense clears phage infections via ssDNA recognition and directional duplex unwindingDruantia recognizes phage ssDNA and drives directional duplex unwinding to clear the infection in a compact anti-phage system.Himpich et al.
• bioRxiv 2026BactoMate: an integrated platform for reproducible bacterial microscopy analysisAn end-to-end toolkit for conversion, segmentation, tracking, lineage QC and reporting of bacterial microscopy datasets.Hallenga et al.
• PNAS 2025Optimization of bacterial flagellum growth for efficient motility and energy consumptionA critical filament-length threshold balances swimming performance against the energetic cost of building the flagellum.Halte et al.
• Nature Communications 2023Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unitCryo-EM reveals how the sodium-driven MotPS stator selects ions and couples rotation to the flagellar rotor.Hu et al.
• J. Biol. Eng. 2024Fluorescent tools for the standardized work in Gram-negative bacteriaA practical fluorescent toolkit for reproducible imaging and genetic work across Gram-negative bacteria.Delgadillo-Guevara et al.

Current funding

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