Advancing next generation genomic tools for discovery of the food microbiome from the field to the store

Funding Organization: USDA / NIFA
Project Duration: Ongoing since 2013

Description: An increasingly number of foodborne outbreaks associated with fresh produce have been observed in the United States. This indicates the vulnerability of our food systems to contamination and public health risk.  The premise of this project is that the next generation of genomic technology will (i) advance knowledge and understanding of the food-environment microbiome through the assessment of viruses as part of the microbial community from the field to the store and (ii) support food safety monitoring practices and ultimately transform how we test. We plan:


(1) To use metagenomics with Illumina sequencing to generate a virome view of various fresh produce (cantaloupe, tomato, lettuce) as well as changes from the field to the store.

(2) To take on a laboratory experiment to examine a seeded bacteriophage consortia during processing and packing of lettuce, to address metagenomic methodology and the potential for changes in the virome.

(3) To use new bioinformatics approaches to analyze the metagenomic fingerprints to assess the microbial ecology of various fresh produce, from the field to the store.

(4) To identify novel viral genetic markers and alternative phage to better inform healthy food systems.

Through the activities mentioned above, our overall project goal is to provide a comprehensive view of the virome of our food from the natural field environment through the built food delivery system, which will guide the efforts towards identification of new targets for monitoring food safety.