Centre for Microbial Single-cell RNA-seq (MICROSEQ)

• Subject Area: Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 503267551

Since its inception in 2013, the Core Unit SysMed of the University of Würzburg has provided next-generation sequencing (NGS) technology and data analysis to a rapidly growing number of local, national, and international users. It has become a role model for managing state-of-the-art research infrastructure, ensuring easy access and reliable service for biomedical researchers at the university and its hospital. SysMed has built strength in RNA-seq based applications, from general gene expression analysis of microbes and eukaryotes, to post-transcriptional control and RNA-protein interactions studies. As we enter a new era of single-cell biology, we aim to develop SysMed as an international hub for NGS based single-cell transcriptomics. Importantly, while single-cell RNA-seq (scRNA-seq) of eukaryotic cells has become routine with commercially available platforms, transcriptomics of individual microbes remains largely uncharted territory. However, thanks to very recent breakthroughs in methodology, including pioneering work from Würzburg scientists, bacterial scRNA-seq is now feasible. This approach promises a new microbiology, for instance, by enabling high-resolution profiling of gene activity in complex microbial consortia such as the microbiome, or monitoring drug susceptibility of pathogens based on RNA signatures from clinical samples. Yet, notwithstanding the success of the initial proof-of-concept studies, bacterial scRNA-seq is in its infancy. To leverage the full potential of single-cell transcriptomics for microbiology and infection research, we propose to set up a Centre for Microbial Single-cell RNA-seq (MICROSEQ). Building on the success of SysMed, MICROSEQ will develop generic protocols for rapid, cost-effective and high-throughput bacterial scRNA-seq, provide state-of-the-art data analysis and visualisation strategies, and offer training opportunities for microbiologists. MICROSEQ is internationally unique in its focus and the collective expertise of the involved scientists, and thereby complements ongoing efforts by DFG to foster the application of NGS technology at German universities.

• DFG Programme: Core Facilities
• Applicant Institution: Julius-Maximilians-Universität Würzburg
• Leader: Professor Dr. Jörg Vogel