Paradigm shift: revolutionizing our understanding of antimicrobial resistance ecology through whole genome analysis of microbial communities

Lead PIs

Morley PS, Belk KE, Yang HUSDA_NIFA_Logo


Booker CW, Boucher C, Bunning M, Burgess BA, Delmore RJ, Gow SP, Hannon S, Jones KL, McAllister TA, McArt JAA, McConnel CS, Noyes NR, Reynolds SJ, Ruiz J, Scott HM, Thomas MG, Van Metre DC, Ward NL, Woerner DR

Funding Agency

United States Department of Agriculture National Institute of Food in Agriculture (USDA NIFA)

Grant Number


Funding Period

2015 – 2018

Lab Personnel

Paul Morley
Noelle Noyes
Jaime Ruiz
Keith Belk
Christina Boucher
Kenneth Jones
Andrea Weinberg
Laura Sample McMeeking
Jennifer Martin
Zaid Abdo
Dale Woerner
Hua Yang


We are experiencing a paradigm shift created by astonishing advances in massively parallel genetic sequencing. High-throughput sequencing is revolutionizing our ability to investigate microbial ecologies, including antimicrobial resistance (AMR). Metagenomics will provide greater insight into the ecology of antimicrobial resistance than was possible using culture-dependent methods. For Goal 1, our broadly interdisciplinary team will optimize use of metagenomic analysis to investigate the ecology of AMR in an integrated series of research projects that leverage existing sample sets. We will investigate the influence of antimicrobial drug exposures on the microbiome and resistome, evaluate a novel approach for source attribution of AMR genes, and evaluate using metagenomics in surveillance for important foodborne pathogens. For agriculture, health sciences, and other life sciences to fully benefit from the revolutionary potential of modern genomics tools, we must provide scientists with greater accessibility to bioinformatics analysis, and improve general science-based literacy for genomics methods. We will address these deficits through outreach (Goal 2), and education (Goals 2 and 3). Activities described in this highly integrated project will aid long-term improvement and sustainability of agriculture by 1) providing an important new perspective on one of the most important public health issues impacting our society – emergence and control of AMR, 2) by developing new tools to help life scientists increase their ability to utilize one of the most revolutionizing technological developments to have occurred, and 3) increasing the science-based literacy of future agriculturists, scientists, and health professionals regarding modern techniques for genomic investigations.