Exploring the dark matter of microbial metabolic interactions and its relevance for bacterial metabolism in a simplified model gut microbiome

• Applicants: Professor Dr. Martin von Bergen; Professor Dr. Christoph Kaleta
• Subject Area: Microbial Ecology and Applied Microbiology ; Bioinformatics and Theoretical Biology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 564414584

Microbial communities in the intestinal tract exhibit complex metabolic interactions critical for their stability and function. However, the mechanisms underlying these interactions, particularly cross-feeding, remain poorly understood. This project investigates the metabolic interdependencies within the simplified SIHUMIx gut microbiome model, consisting of eight bacterial species extended by the bacterial species Eggerthella lenta, to elucidate the relevance and flexibility of cross-feeding interactions. Using the innovative Species-Specific Partitioned Co-Cultivation (S-PECOC) system, we aim to track metabolite exchanges at a species-specific level under controlled conditions. Coupled with innovative metabolic modeling approaches, we will systematically analyze the dependence of community members on cross-feeding, the rewiring of metabolic networks following species loss, and the extent of metabolite exchange in complex ecosystems. Experimental and computational insights will be integrated to reconstruct a comprehensive cross-feeding network, shedding light on metabolic pathways that sustain community stability and resilience. This research will enhance our mechanistic understanding of microbial metabolic cooperation, providing a foundation for microbiome-based therapies and ecological engineering applications.

• DFG Programme: Priority Programmes
• Subproject of: SPP 2474: Illuminating gene functions in the human gut microbiome