Microbiome Evolution Under Antibiotic Pressure

Antimicrobial resistance (AMR) is a growing global health threat, fueled by spontaneous DNA mutations and horizontal gene transfer (HGT) via mobile genetic elements such as plasmids and phages. The human gut microbiota—comprising hundreds of co-existing bacterial populations—may serve as a hotspot for the emergence and spread of resistance due to its density and complexity.

This project investigates how antibiotic exposure perturbs gut microbial communities and promotes AMR evolution and spread. Using high-resolution longitudinal sampling and advanced molecular tools—including long-read metagenomic sequencing and chromosome conformation capture (Hi-C)—we reconstruct the dynamic genomic landscape of the gut under selective pressure.

By studying the community as an integrated system, we aim to uncover how resistance traits arise and disseminate across interacting strains and species. Our goal is to quantify the role of the gut microbiome in promoting AMR and to inform strategies that balance effective treatment with long-term public health outcomes.

Project Summary:

The Evolution and Spread of Antimicrobial Resistance

More Information:

Project Funding
 

National Institute of Allergy and Infectious Diseases

 

 

Thomas C. and Joan M. Merigan Endowment at Stanford University

 



Research Team

Eitan Yaffe
Research Scientist
Chen Gui
Research Assistant
Shachar Katz
Research Assistant