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University of Wisconsin–Madison

The Tomato Microbiome in Sickness and in Health

This project will help researchers understand how the susceptibility of a plant host affects its microbiome and identify ways that the plant microbiome can be measured and manipulated to improve food safety and agricultural sustainability.

The plant host in this study is the tomato, an established model system and a high-value crop, growing in commercial conditions in Florida, which is the most important tomato-growing region in the United States. The likelihood that microbiome structure plays roles in tomato disease resistance is high, and this study looks into questions about the role of the tomato microbiome in disease resistance and susceptibility. The specific questions this study asks are: How does disease perturb the microbiome of healthy tomato plants? How does broad-spectrum disease resistance shape the tomato microbiome? How does the structure of the pre-infection microbiome influence infection by plant pathogens?

The experimental design uses a set of transgenic (isogenic) tomato lines that differ in their disease resistance. The study will assess microbiomes in three discrete niches in each plant: the leaf surface, the xylem sap, and the rhizosphere. Studying a commercial crop under field conditions will facilitate near term translational application.


Jeri Barak-Cunningham, Associate Professor of Plant Pathology


Caitilyn Allen, Professor of Plant Pathology

Richard Lanikau, Assistant Professor of Plant Pathology


Jeffrey Jones, Professor of Plant Pathology at the University of Florida

Mathews Paret, Assistant Professor of Plant Pathology at the University of Florida