Time- and position-specific analysis of S. Typhimurium metabolism in the infection process of mice

• Applicant: Christopher Schubert
• Subject Area: Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology ; Metabolism, Biochemistry and Genetics of Microorganisms
• Term: since 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 495839694

Dysfunction of the microbiome can lead to disruption and deterioration of mammalian health, such as intestinal inflammation. This is associated with an alteration in the composition of the gut microbiota, known as dysbiosis, which allows facultative anaerobic bacteria such as Salmonella spp. to thrive. Ex vivo physiology precisely defines metabolic states such as nitrogen limitation and saturation. However, this constancy is largely absent in vivo due to the diverse and heterogeneous environment of the mammalian gut. One goal will be to apply our extensive knowledge of ex vivo physiology and regulation to the S. Typhimurium infection process in order to identify time- and position-specific situations in which S. Tm. faces specific metabolic challenges. The importance of the three glycolytic degradation pathways, Embden-Meyerhof-Parnas pathway (EMP), Entner-Doudoroff pathway (ED) and oxidative pentose phosphate pathway (OPP) in the context of S. Tm. growth in healthy and inflamed gut will be investigated. In addition, fluorescence reporter assays and microscopy will be used to characterize available carbon sources and the nitrogen status of S. Tm. to provide a more comprehensive picture of S. Tm. metabolism during the infection process in the mouse intestine. Competitive infection experiments can be used to measure fitness defects of specific mutants or phenotypes in the environment shaped by an isogenic wild-type control. The main problem with this approach is that it averages an entire population of bacteria. To capture spatial differences in the individual fitness of mutants and thus achieve a deeper level of characterization, I will develop a fluorescence in situ hybridization (FISH) labeling and detection method for gut lumen mutants of S. Tm. strains. This allows the localization of S. Tm. wild-type and mutant strains in different intestinal microenvironments and answers the question whether the mutants colonize different sites in the intestinal lumen to escape metabolic impairment and continue to grow. Oligo mouse microbiota (OligoMM, 12 strains microbiota isolates) and low complex microbiota (LCM, 8 strains of altered Schaedler flora) mice will be used for experiments because these recapitulate key physiological and functional features of a complex mouse microbiome. The improved understanding of the physiology of S. Tm. in vivo, may reveal vulnerabilities of the pathogen and thereby identify points susceptible to external intervention, opening up new avenues for prevention or therapy of this common infectious disease.

• DFG Programme: WBP Fellowship
• International Connection: Switzerland
• Host: Professor Dr. Wolf-Dietrich Hardt