PhD position - Reprogramming bacteria

Department/Institute: Faculty of Biology, Microbiology

Subject areas/Research fields: Microbiology, Molecular Biology

Keywords: genetic engineering, Desulfovibrio spp., synthetic bacterial communities

Name of supervisor: Prof. Dr. Kirsten Jung

Funding: third party funding through the research group (BioSysteM) or DAAD-GSSP (LSM)

Project title: Reprogramming bacteria

Project description: The human gut microbiota plays an important role in health and disease. Trillions of microorganisms, including bacteria, yeasts and viruses, the so-called commensals, live in the human digestive system in symbiosis with the host and support its health. In the healthy adult gut, the commensal bacteria are dominated by obligate fermenting bacteria of the phyla Firmicutes and Bacteroidota. A weakening of host functions that control parameters important for microbial growth generates abnormal growth conditions and niches for some bacteria, such as Desulfovibrio spp., which then harm the host.

In this project, we will:

1. Identify species-specific essential genes that can be targeted by a gene-editing approach.
2. Reprogram bacteria by gene-editing in synthetic bacterial communities.

We will develop and use a combination of genetic engineering methods, multi-omics approaches (transcriptomics, proteomics), and microbial assays (pairwise bacterial interactions, anaerobic synthetic consortia).

Reprogramming bacteria could pave the way to restoring a healthy gut microbiota in humans.

Strong experience in molecular biology and anaerobic cultivation techniques is required.

References:

• Almeida, L., Fajardo-Ruiz, E., Brameyer, S., Jung, K. (2025) The framework for genetic engineering in Desulfovibrionaceae. ACS Synth. Biol., 14: 2445−2454 https://doi.org/10.1021/acssynbio.5c00351
• Schumacher, K., Gelhausen, R., Backofen, R., Kion-Crosby, W., Barquist, L., Jung, K. (2023) Ribosome profiling reveals the fine-tuned response of Escherichia coli to acid stress. mSystems, Nov 1:e0103723. doi: 10.1128/msystems.01037-23
• Ronda, C., Perdue, T., Schwanz, L., Gelsinger D. R., Brockmann, L., Kaufman, A., Huang, Y., Sternberg, S.H., Wang, H.H. (2025) Precise virulence inactivation using a CRISPR-associated transposase for combating Enterobacteriaceae gut pathogens. Nat. Biomed. Eng. https://doi.org/10.1038/s41551-025-01453-1

For further information, please contact: Prof. Dr. Kirsten Jung, jung@lmu.de

Research group website: https://www.bio.lmu.de/en/research/research-fields/microbiology/

Apply: Please send your application through the online portal of the Graduate School Life Science Munich (LSM)