Microbiome diversity protects against pathogens by nutrient blocking: metagenomic sequencing and whole genome assembly of an E. coli clinical isolate

Diverse gut microbiomes are associated with health benefits, including protection against pathogens. Many mechanisms exist that contribute to this protection, but they are often context-specific. In this project, we used an ecological approach to demonstrate that diversity of the microbiome protects against pathogens by increasing the probability that the microbiome overlaps in nutrient utilization requirements with a gut pathogen that is attempting to colonize. We used this principle, termed nutrient blocking, to correctly predict which communities would be protective against specific pathogens.This BioProject contains metagenomic sequencing data from gnotobiotic mouse experiments to validate our findings in realistic experimental models, and an assembly of a clinical isolate of Escherichia coli that we used to test our hypotheses.