Plant-microbe interactions: data integration

The soil is a reservoir of microorganisms, which play key roles in ecosystems and can improve plant growth and health. Moreover, plants exert selective forces on the soil microbial communities through root exudation, which is an input of organic carbon into the soil, where it is directly available for microbial growth. However, the root exudate is also composed of specific compounds, which play an important role as signaling molecules in root-microbe interaction. We know that the composition of root exudates varies with the environmental conditions, the plant developmental stage, plant species and cultivars, and as a result so does the plant microbiome. Meantime, the molecular mechanisms involved in the microbiome selection by the plant are still poorly understood.

The aim of our research is to better understand how plants can select a beneficial microbiome under abiotic/biotic stress and find new lever to improve plant stress tolerance by identifying candidate genes, metabolites and microorganisms. To do so, we are using and developing new data analysis and computational tools in order to analyse and integrate phenotypic and omics data, such as genomics, transcriptomics, metabolomics and metagenomics.

Scientists involved in this research

Johan Westerhuis
Harro Bouwmeester
Daan Mangé
Bora Kim
Age Smilde
Lemeng Dong
Sébastien Jaupitre
Benjamin Thiombiano
Fred White
Anna Heintz Buschart


  1. Integration of omics data to unravel root microbiome recruitment

    Anouk Zancarini, Johan A Westerhuis,  Age K Smilde and Harro J Bouwmeester, Current Opinion in Biotechnology 2021, 70:255–261 doi:10.1016/j.copbio.2021.06.016

  2. Metabolic interactions in beneficial microbe recruitment by plants

    Davar Abedini,, Sébastien Jaupitre, Harro Bouwmeester and Lemeng Dong, Current Opinion in Biotechnology 2021, 70:241–247doi:10.1016/j.copbio.2021.06.015