The role of the microbiome in pesticide – host interaction

Background

Farmers rely on pesticides to maximise their yields. However, some pesticides are potentially harmful to environmental, plant, animal, and human health. The bacteria in our gut are impacted by pesticides, while at the same time the bacteria can metabolize pesticides and influence the impact of pesticides on the host. This project if part of SPRINT (https://sprint-h2020.eu/).

Objectives

In this bioinformatics project, we investigate the interaction between pesticides and the human gut microbiome. Metagenomics, metabolomics, and host health parameters will be combined to identify microbial genes implicated in the conversion of or resistance to pesticides, and to look for metagenome features that might (partially) explain why the link between pesticide exposure and blood pesticide levels varies between individuals.

Methodology

This is an in-silico project, without wet-lab activities. Available data includes faecal metagenome and pesticide profiles of 600 individuals from 11 different countries. We will apply a range if bioinformatics techniques, ranging from metagenome assembly to multivariate correlation analysis, to generate hypotheses on the interaction between pesticides, microbiomes, and host health. Most of the work will be done in Linux, using Python for simple automation and Python and / or R for data analysis.

Requirements

We are looking for BSc/MSc students in the field of Biology, Microbiology, or related fields. We expect that the student has experience with Linux and Python or has affinity with data analysis and the interest to learn. The project will have a duration between 3 and 6 months.

Contact information

Supervisors are Maaike Gerritse (email:maaike.gerritse@wur.nl), PhD candidate, and Jos Boekhorst, staff scientist at Host-Microbe Interactomics, Wageningen University and Research. Visiting address: Room E1205, De Elst 1, 6708 WD, Wageningen.