VETMD Vet Population Med
College of Veterinary Medicine
College of Veterinary Medicine
Metagenomics (Microbiome and Resistome)
Antimicrobial resistance is a complex ecological and population genetic phenomenon of microbes, with potentially dire consequences for human and animal health. The Noyes lab strives to:
- Advance understanding of how antimicrobial resistance develops and persists in both microbial and host populations
- Investigate applied, practical measures to effectively mitigate and control antimicrobial resistance
- Improve risk assessment of antimicrobial resistance from different spheres in society (e.g., human hospitals, veterinary medicine, livestock production)
View antimicrobial resistance as both a "natural" and anthropogenically mediated process
These researchers work with many different types of data, but in all cases their goal is to turn the data into usable and useful information. Some examples of this include:
- Use of Bayesian Network Analysis for evaluation of disparate, hierarchical microbiome data
- Development of bioinformatic pipelines for both metagenomic and WGS analysis
- Curation of an antimicrobial resistance database and ontology specifically for metagenomic data
- Development of modeling techniques for risk assessment (i.e., identifying associations between antimicrobial use and resistance)
The lab specializes in using metagenomic data to improve understanding of the ecology of antimicrobial resistance, aka the "resistome" (i.e., all antimicrobial resistance genes within a given sample):
- How does the resistome change within and between livestock production systems?
- How can we increase the sensitivity and specificity of the metagenomics approach?
- How can metagenomic data be used to identify pathogens from a food safety perspective?
Projects ongoing in the lab:
- Livestock production is an integral part of our world. Contact between livestock and humans can be direct and indirect, occuring through the food chain and the environment. Our lab is particularly interested in how livestock production systems exchange microbes and DNA across environmental interfaces:
- What role do wastewater and manure sustainability practices play in this potential transfer?
- Do antimicrobial use practices impact the transfer of antimicrobial resistance through environmental routes of exposure?
- Food safety is the cornerstone of a healthy society. These researchers investigate comprehensive, systems-based approaches to improving both pre- and post-harvest food safety:
- Impact of multiple-hurdle interventions on post-harvest levels of pathogens and antimicrobial resistance
- Impact of antimicrobial drugs on antimicrobial resistance in pre-harvest animal pathogens and indicator organisms
- The microbiome is crucial to the health of animal, humans and the planet. While we often think of microbiomes in terms of the body (e.g., the "gut microbiome"), non-living environments also contain microbiomes (e.g., the microbiome of the "built environment"). This lab is interested in understanding how these various microbiomes influence livestock production, food safety and animal/public health.
Jarno Niklas Alanko
Irene Bueno Padilla
Gerardo Diaz Ortiz
Tara Nath Gaire