2026 Gut Microbiota International Grant Winner

The human gut microbiome constitutes a densely interconnected ecological system that plays a pivotal role in host metabolism, immunity, and overall physiological homeostasis. While the gut ecosystem is generally resilient, capable of resisting perturbations and recovering its compositional and functional baseline, key mechanisms underlying this resilience remain insufficiently characterized. Existing longitudinal and interventional studies suggest that the microbiome is typically stable at the ecosystem level but can undergo rapid shifts following acute perturbations such as dietary changes or antibiotic exposure. However, most prior work lacked sufficient temporal granularity, comprehensive phenotyping, or strain-level resolution to disentangle the ecological, metabolic, and host-driven determinants of stability, resistance, and recovery. 

We hypothesize that ecosystem resilience emerges from  dependencies and complementarity between gut microbiome members up to the strain-level, with resilience and recovery dynamics being linked to the individual local environmental context specific to the host. To this aim, we will first investigate determinants of (in)stability by observing real-world perturbations in an unprecedented existing, densely sampled longitudinal population cohort, capturing distinct (type, duration, magnitude) and possibly cumulative stressors.

Second, we will precisely assess ecological and host resilience patterns and responses using data from a unique interventional study with series of acute dietary perturbations at high temporal resolution. Finally, we will study identified trajectories and patterns in mechanistic experiments to disentangle how underlying taxonomic and metabolic interactions as well as (strain level) redundancies underlie observed resilience. 

Question to Prof. Jeroen Raes

What will the Biocodex Microbiota Foundation and this grant bring to your research project?

We’re extremely happy with the Biocodex Foundation support! The grant is unique in the sense that it allows us to address fundamental microbial ecology questions regarding microbiome resilience; such work is generally underfunded but super important for all future microbiome therapies. So we warmly thank the foundation and the jury for appreciating the importance of basic research to complement clinical studies.