Metagenom Bio Life Science – Culture Independent Testing and Monitoring for Controlled Environment Food Safety and Crop Protection

Project supported by the Phytobiomes Alliance

Funded by

Ontario Ministry of Agriculture, Food and Rural Affairs, Ontario Agri-Food Research Initiative


2 years


August 2020 - July 2022


Trevor Charles, Waterloo Centre for Microbial Research


Project Overview

Control of pathogenic, disease causing microbes is especially critical in vegetable production systems, where the product is often subject to minimal processing before consumption. Hydroponic controlled environment production systems such as greenhouses and indoor farms that employ soilless cultivation with liquid nutrient distributed through fertigation systems have great potential for microbial control, while also providing a conduit for distribution of contaminating pathogens throughout the system. The proposed work aims to refine and implement rapid culture-independent monitoring for controlled environment vegetable production systems, with capability to track both crop disease causing organisms and food borne human pathogens. Widespread adoption of such a monitoring program by Ontario vegetable growers would contribute to more accurate and efficient crop disease and food safety control, resulting in increased yield and quality, reduction of waste, and improved food safety management.


  • Construct a database of microbiome profiles of operating commercial hydroponic systems in Ontario
  • Develop a novel hybrid sequencing method, MetaMicroBiomics, for robust, accurate and sensitivemicrobiome monitoring
  • Identification of key marker genes for hydroponic systems using shotgun metagenomics data
  • Construct a current overview of emerging sequence-based and protein-based technologies for rapid / on-site / continuous biomarker monitoring

Key personnel

Trevor Charles (Waterloo Centre for Microbial Research)

Michael Lynch, Metagenom Bio Life Science, Canada

Rebecca Co, Metagenom Bio LIfe Science, Canada