Metabolic profiling of the microbiota

Bacteria play a central role in health and disease. While many microbial species perform essential functions in the host, others can contribute to infection and chronic inflammatory conditions. A key unresolved question is how metabollically active bacteria are in different niches within the living organism and how their activity is shaped by, or in turn shapes, the immune system. Current methods largely provide indirect measurements or population averages and do not allow precise identification of metabolically active or proliferating individual bacterial cells in vivo.The objective of this project is to establish and apply novel approaches to directly assess bacterial proliferation and metabolic activity within the living host, and to investigate their interaction with the immune system. We hypothesize that the immune system selectively recognizes and regulates metabolically active and proliferating bacteria, and that this regulation differs depending on host factors such as age, immune status, and inflammatory disease.To address this, we will combine two complementary labeling strategies: (i) incorporation of a nucleoside analog into the DNA of proliferating bacteria, and (ii) incorporation of stable isotopes in metabolically active bacteria. This combined approach enables the identification and quantification of actively growing and metabolically active bacterial populations in vivo.Experiments will be performed in mouse models, including wild-type, immunodeficient, and gnotobiotic animals with defined microbiota. To investigate bacterial activity under inflammatory conditions, established disease models will be employed, including dextran sulfate sodium (DSS)-induced colitis as a model for intestinal inflammation and collagen-induced arthritis (CIA) as a model for systemic autoimmune disease. Labeling substances will be administered via injection or drinking water using minimally invasive procedures. In the short term, this project will provide new methodological and scientific insights into bacterial activity in vivo and its relationship with the immune response. In the long term, the results may contribute to a better understanding of host–microbe interactions and support the development of future diagnostic and therapeutic strategies targeting microbial communities in inflammatory and autoimmune diseases.