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Metagenomics of Fusarium Head Blight of wheat

Principal Investigator

David Guttman & Gopal Subramaniam

Research Institution

University of Toronto / Agriculture and Agri-Food Canada

External Funding Partners

Agriculture and Agri-Food Canada (Microbiome & Metatranscriptome grant); Compute Canada Resource Allocation Competition (RAC)

Project Start

April 2017

Project End

March 2020


  • Catalogue and monitor behaviour of natural microbial endophytes and epiphytes on wheat heads by:
    • Assessing natural variation of microbial populations in resistant versus susceptible wheat varieties;
    • Determining dynamics of microbial populations and their behaviours after Fusarium graminearum infection; and
    • Identifying potentially beneficial microbes that may influence the course of the F. graminearum infection process.


  • The identification of potential yield-promoting members of the wheat head microbiome when the wheat head is infected with FHB (Fusarium Head Blight) will help guide our future research focused on identifying and developing novel biocontrol agents to protect wheat against FHB.
  • The improved knowledge of the host/pathogen interaction in the context of natural microbiome found on the wheat head will greatly improve our ability to combine natural resistance strategies or interfere with disease development using sustainable crop management protocols (e.g. biological control).

Scientific Summary

Fusarium head blight (FHB) is a devastating global disease of small grain cereals that has been called “the worst plant disease to hit the US since the rust epidemics in the 1950s”. The disease is caused by the fungus Fusarium graminearum, which overwinters in crop debris and infects grain heads under favorable environmental conditions. FHB poses a double threat. First, it can significantly reduce both yield and seed germination by discoloring and shriveling the grain kernels. Second, the pathogen produces mycotoxins that contaminate grains during infection, and which are a very direct health risk to humans and domesticated animals. The severity of FHB infection depends on the cereal variety, amount of fungal inoculum and favorable weather conditions. The most effective control strategies have relied on the use of resistant varieties and fungicides; however, these control measures are not always effective, resulting in massive crop losses or contaminated grain. Consequently, there is very strong interest in the identification and development of novel biocontrol agents that can assist in the fight against this disease.

The goal of the project is to understand the contribution of microbial communities to the health of wheat plants. During the study, microbial communities called microbiomes will be assessed to determine how they differ among cultivars with different levels of FHB susceptibility, and determine how the microbiomes respond to F. graminearum infections and the development of FHB disease. This study will provide the first look at the microbiological changes that occur during the FHB development. It will assess the impact of both host (wheat) and pathogen genetic variability on FHB disease development. Understanding the wheat head microbiome and the dynamics of this community during FHB disease development has the potential to reveal new pathogen antagonists or growth promoting microbes, and thereby facilitate the identification of novel biocontrol agents.