Genetic drivers of the spatial ecology around dietary substrates

• Applicant: Dr. Martin Thomas Jahn
• Subject Area: Microbial Ecology and Applied Microbiology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 564415106

The gut microbiota plays a critical role in human health by fermenting dietary fiber into beneficial metabolites such as short-chain fatty acids (SCFAs). However, interactions between gut microbes and fiber are complex and poorly understood, which hinders the development of targeted microbiome-based therapies. This project aims to bridge this gap by investigating the genetic, spatial, and temporal organisation of fiber degradation in the gut. To achieve this, we will employ advanced imaging techniques to map the functional organisation of the gut microbiota in relation to defined fiber particles and conduct in vivo and in vitro experiments to establish causal relationships between genes and fiber degradation. Our research is structured into three interconnected but independent work packages: (1) Characterising the spatial genomics of in vivo fiber degradation by mapping the in situ spatial relationships between key gut microbes and dietary fibers and identifying gene functions related to fiber binding and degradation; (2) Investigating the spatio-temporal dynamics of fiber degradation, tracking bacterial populations as they transition from planktonic to fiber-bound states, and analysing the genetic and regulatory mechanisms governing these processes; and (3) Studying the spatial ecology of fiber degradation, exploring how interspecies interactions, such as syntrophy and competition, influence the spatial organisation and efficiency of fiber degradation. Ultimately, this will provide a foundation for the targeted manipulation of gut microbial communities to improve health outcomes. Whilst generating massive interaction potential with SPP 2474 groups (see Project integration into SPP 2474), our programme fits squarely to the core objectives of SPP 2474 by focusing on understanding the unexplored functions of genes in key human gut bacteria and by moving beyond descriptive associations to mapping causal mechanisms.

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