Understanding and engineering complex microbial communities

The human gut’s natural microbial shield against dangerous bacteria often collapses under antibiotic treatment, leaving patients vulnerable to infections like Salmonella. This project aims to design synthetic microbial communities that remain stable and protective even when antibiotics are present. The problem is that the gut’s ecosystem is staggeringly complex—dozens of bacterial species interact, compete, and evolve in ways that make their collective behaviour nearly impossible to predict. Current probiotics are too simple to fill the gap. This research will first build mathematical theory and computational tools to model these interactions, then test those models by engineering lab-grown gut communities that resist both antibiotics and pathogen invasion. Finally, the team will move into live mice to see whether the engineered communities can block Salmonella infection in a real body. If successful, this work could lead to a new class of “designer” probiotic therapies—microbial cocktails tailored to restore colonisation resistance after antibiotic courses, reducing hospital-acquired infections and the need for further antibiotics. The project is fundamentally curiosity-driven, tackling the deep challenge of predicting complex biological systems. Past fundamental work on microbial ecology has already transformed wastewater treatment and agriculture; a similar understanding of the gut could eventually reshape how we manage infection risk in vulnerable patients.