Abstract

 

The vertebrate intestine is the primary habitat of Escherichia coli, a species ranging from commensal to pathogenic and central to many biological discoveries. Humans can be colonized by multiple strains simultaneously, yet the eco-evolutionary forces shaping which persist remain poorly understood. This thesis investigates how phenotypic diversity, rooted in genetic variation, influences a strain’s ability to compete and survive, explaining why only a limited subset persist long-term while others remain transient. We applied CRISPR-based DNA barcoding to natural isolates, enabling multi-strain competition assays across ecological scales: minimal media, ex vivo MBRA gut models, and mouse colonization. Tracking 26 barcoded isolates, including multiple ST131 strains, we found that in complex systems early competition outcomes were highly deterministic. Over longer timescales, however, de novo mutations introduced stochastic reshuffling, even among closely related isolates. Simplified in vitro assays, supported by Lotka–Volterra modeling, revealed positive and negative interactions between near-identical strains that diverged only ~100 years ago. These results highlight the fluidity of E. coli competitive hierarchies and underscore the importance of studying multiple isolates per lineage to capture eco-evolutionary diversity.