Project Overview

Healthy Hydroponics is a project founded and led by Dr. Trevor Charles, of Metagenom Bio Life Science Inc., a company that provides DNA sequencing and bioinformatics services to a variety of academic researchers and industries, with a focus on the agriculture and environment sectors. Control of pathogenic, disease causing microbes is especially critical in vegetable and cannabis production systems, where the product is often subject to minimal processing before consumption. Hydroponic systems in controlled-environment agriculture 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 plant pathogens and food-borne pathogens throughout the system.

Our project aims to refine and implement rapid culture-independent monitoring for controlled environment vegetable production systems, with capability to track both plant pathogens and foodborne 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
  • Develop a novel hybrid sequencing method, MetaMicroBiomics, for robust, accurate and sensitive microbiome 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

Participate in our Project

We are excited about working with growers operating all types of hydroponic systems, be they greenhouses, indoor, or vertical, producing any type of crop. We will consult with you before and after sampling, so that we can design a sampling strategy that is customized for your operation. Our sampling methods are non-destructive, and we will share all data from your farm with you. If you are interested in finding out what is in the microbiome of your system, give us a shout.

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