The group, established in March 2018, applies high-throughput RNA-seq approaches to complex infection settings comprising of enteric bacterial pathogens, their mammalian hosts and the resident gut microbiota. The aim is to identify and molecularly characterize novel noncoding RNAs and RNA-binding proteins with potential roles in bacterial virulence or the protection against pathogenic attack.

Dual RNA-seq
Infectious diseases caused by pathogenic microbes constitute a major public health threat. We find ourselves in the middle of an antibiotic crisis and there is urgent demand for novel therapeutic strategies to combat bacterial pathogens. The interaction of bacterial pathogens with mammalian hosts and their resident microbiota represents an incredibly intricate biological process, involving numerous organisms from different kingdoms of life, all actively contributing to the balance between pathogenesis and clearance. We can only fully comprehend – and eventually treat – infectious diseases, once we understand the role of each of the organisms involved.             
The transcriptome provides a global snapshot of the physiological state of a cell under a given condition. Accordingly, genome-wide transcriptomic approaches are commonly used to deduce cell states, both in bacterial and eukaryotic systems. For example, high-throughput transcriptome sequencing (RNA-seq) has been applied to virtually every biological process studied, including bacterial infections of mammalian hosts. However, to account for the widespread differences between bacterial and eukaryotic transcriptomes, original gene expression studies of infection focused either on the pathogen or its host. To achieve a better understanding of host-pathogen interactions, we have recently pioneered a novel RNA-seq-based technology, Dual RNA-seq, which measures host and pathogen gene expression simultaneously during infection. This work has also contributed to a deeper understanding of the role of regulatory non-coding RNA in bacterial virulence and host immunity.

Application of multi-organism RNA-seq approaches to bacterial infections. Left: Microscopy image of human epithelial cells (cytosol in red; nuclei in blue) infected with the enteric pathogen Salmonella Typhimurium (green). Right: Concept of Dual RNA-seq, that measures gene expression during infection simultaneously in the infecting pathogen and its infected host

In-vivo RNA-seq            
In vivo, pathogenic bacteria do not interact with their host cells in isolation, but in the presence of the protective commensal bacteria collectively referred to as the microbiota. The group focuses on applying RNA-seq approaches to complex infection models of bacterial pathogens and their hosts, as well as resident commensal species, to analyze the dynamic interplay of the host and its microbiota with invading pathogens. For example, using Salmonella Typhimurium as a pathogenic model bacterium, we track infections in defined mouse models colonized with different gut microbial consortia by taking RNA samples at defined time points after infection and from different biological sources (ceacum, colon, stool samples). In parallel, genomic DNA samples are analyzed to discriminate between changes within the microbial composition and gene expression differences during infection. By comparing pathogen, host and microbiota transcriptomes upon wild-type infection to that with defined Salmonella mutants, we aim to identify and correlate gene expression changes between the interaction partners. This will reveal novel inter-species interactions and potential consequences of individual bacterial virulence factors for overcoming the microbiota-host barrier. Similarly, by changing the microbiota composition or using deletion strains of select commensal species, this will reveal the molecular impact of a given consortium member in the host and pathogen transcriptome.


"Theta Base"

RNA biology of Bacteroides thetaiotaomicron 
The anaerobic Bacteroides thetaiotaomicron represents one of the most prevalent members of the gut microbiota. While techniques are available to genetically manipulate this bacterium, and its proteome and metabolome are subject of intense study less is known regarding its transcriptome. We will apply various RNA-seq-based approaches to B. theta grown in vitro under a set of defined conditions, in order to compile a high-resolution transcriptome annotation for this important microbiota member and identify non-coding RNA candidates with a likely role in colonization resistance.