Eisenreich and his co-workers are studying metabolic pathways and fluxes in bacterial pathogens since more than 20 years. Kicked off by the former DFG priority program SPP1316, Eisenreich and his co-workers became welcome partners for many microbiologists on a national and international level in sharing their technologies and expertise to determine metabolic pathways and fluxes on the basis of ¹³C-labelling experiments and metabolomics. In the past years, the basic methods of ¹³C-isotopologue profiling could be optimized as a platform technology for the analysis of pathogenic microorganisms and their host cells/organisms. This technique could open new avenues to study metabolisms of pathogens and their infected host cells/organoids/tissue/animals.