NutriGut · Decoding Nutrient Preferences to Shape Resilient Microbial Communities

The human gut microbiome plays a central role in health by contributing to digestion, immune regulation, and protection against pathogens. However, the ecological principles governing its assembly, resilience, and colonization resistance remain unclear. Nutrient competition has emerged as a key driver of community structure and pathogen exclusion.The NutriGut project aims to unravel how microbial nutrient preferences shape gut microbiome assembly and how key species influence resilience to environmental stressors. Using defined communities, I will (1) characterise nutrient preferences and their role in community assembly, (2) assess how antibiotics and pathogens affect nutrient-driven interactions and resilience, and (3) validate key species’ roles in microbiota resilience and colonization resistance in vivo.The project integrates high-throughput in vitro screening, synthetic microbial ecology, molecular and multi-omics (qPCR, proteomics, metabolomics), and mouse models. By profiling nutrient use in monocultures and communities and applying stressors, it will clarify how resource competition governs microbiome dynamics and stress resilience.This project will deliver a mechanistic, predictive framework for how nutrient preferences govern microbiome assembly, stability, and colonization resistance. I will identify key species/consortia, along with their nutrient utilization pathways, driving pathogen resistance and validate their efficacy in vivo. These insights will enable the rational design of protective microbial consortia and targeted nutritional interventions, ultimately advancing the frontier of precision microbiome science. Performing this research in Prof. Stecher’s lab, a leader in microbiome ecology and colonization resistance, will be instrumental in enhancing my scientific independence, interdisciplinary expertise, and leadership, positioning me as a strong candidate for a leading independent research position.