Universiteit Leiden

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Research project


Steering soil microbiomes for better crop quality: the holy grail to improve human health?

2023 - 2029
Martijn Bezemer

Research question

  1. How does the intensity of soil management affect soil microbiomes and their functionality?
  2. How does the soil microbiome affect plant microbiomes and nutritional quality of crops grown in this soil?
  3. How does crop quality and its microbiome composition affect gut microbiomes and human health?


Human gut health and the gut microbiome play important roles in the pathogenesis of non-communicable diseases (NCDs). Modulating the gut microbiome to improve gut health may therefore prevent these NCDs. Food is the primary driver of gut microbiome. Because soil use and the soil microbiome affect the nutritional quality of food, we predict that soil use and gut health are closely interlinked.

Decades of intensified agriculture to maintain high yields have relied on high inputs of pesticides and fertilizers. However, this is environmentally unsustainable because it damages soil health. We further hypothesize that these assaults to soil health directly harm our gut microbiome and our gut health, thereby increasing our risk of NCDs. Using a combination of approaches from experimental, clinical and social sciences, we will first determine how different agricultural practices, measured in terms of land use intensity, affect the soil microbiome. Next, we will examine how these practices affect the microbiomes, metabolites and nutritional properties of the crops we eat. These crops will then be evaluated in terms of taste by consumers, and for their effects on human gut function and gut health. Finally, we will study consumer perspectives of healthy food and their acceptance of microbiome optimized crops.

Our interdisciplinary consortium includes partners from universities, universities of applied sciences, research/ knowledge institutes, farmers, consumers and companies. The desired impacts of our coordinate efforts are to: improve consumer health, improve soil health and agricultural sustainability, and ensure economic well-being for farmers.

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