In situ single-cell metabolic profiling of the microbiota and its control by the immune system

• Applicants: Professor Dr. Hyun-Dong Chang; Dr. Andrey A. Kruglov
• Subject Area: Medical Microbiology and Mycology, Hygiene, Molecular Infection Biology ; Immunology ; Microbial Ecology and Applied Microbiology
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 545888192

Differences in physico-chemical conditions, interaction with the mucosal immune system and nutrient gradients shape the composition and activity of the microbiota along both longitudinal and cross-sectional axes of the intestine. While the identity of the microbes inhabiting different parts of the intestinal tract is well studied, we lack an understanding of the microbial activity landscape along the gut. Metabolic activity of bacteria is linked with functionality, e.g. proliferation, production of host- and microbial community-relevant metabolites. We hypothesize that metabolically active bacteria are spatially stratified and interact more actively with the host to maintain homeostasis and that perturbation of this system contributes to disease. This project aims to gain a functional understanding of the spatial organization of the gut microbiota in situ at an unprecedented resolution, i.e. on the single cell level. For this, we have defined three objectives. (1) We will map the microbial metabolic activity along the intestinal tract of mice in situ over time by employing general tracers of metabolic activity and Raman microspectroscopy to quantify microbial activity with single cell-level resolution in a spatial context. This we will correlated to bacterial phenotyping profiling IgA coating and surface sugar expression and phylogenetic identification. (2) We will dissect how the microbial phenotypic, compositional and metabolic spatial structure is regulated by different immune components interacting with the microbiome, i.e. immunoglobulins, T and B cells, and TNF-regulated inflammation. In a translational approach, we will on the single cell level link microbial phenotype, IgA coating and metabolic activity in human (fecal) samples ex vivo in health and in patients with rheumatoid arthritis. (3) We will directly target the functional activity of specific bacteria using originally developed monoclonal IgA antibodies and assess its impact on bacterial community activity and interactions, both in vivo and in 3D-printed model communities. Thus, this project will help to elucidate the ecological and functional interactions within the intestinal environment, with spatial stratification, and with the host in the context of homeostasis and when perturbed in chronic inflammation. This proposal brings together an interdisciplinary team and collaborators with complementary expertise in immunology, microbiology, imaging, physics and microbial single-cell analyses techniques optimally suited to address this aim. Created knowledge will unveil new possibilities to manipulate the microbiome to support health, for instance by designing targeted interventions to specifically shape microbial communities in the gut.

• DFG Programme: Research Grants
• International Connection: United Kingdom
• Cooperation Partners: Fatima Cardoso Pereira, Ph.D.; Professor Sumeet Mahajan, Ph.D.