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Prior to starting her PhD, Naomi concluded her MSc at Wageningen University, specialising in Ecological Modelling and minoring in Chemical and Microbial Ecology at Cornell University. During her MSc, she researched methane uptake by soil microbes at the Dutch Institute of Ecology (NIOO, research intern in the Paul Bodelier Group), where her interest in microbial ecology further solidified. In 2018, Naomi was nominated and selected to be one of Europe's 100 Top Life Sciences students invited to the Roche Continents Summer School. During her MSc, she was active in local (Dutch Student Union), national (Think Tank Dutch Ministry of Foreign Affairs) as well as international (United Nations) politics, aiming to increase public access and support for science and education.

Research Interests:

Naomi's PhD covers the topic of Mathematical Modelling of Microbial Community Interaction Dynamics, focussing on how available experimental data can be best utilised in ecological models to unravel intriguing unknowns in the microbial world; particularly that of the gut. A better grasp on mechanisms shaping the interaction landscape of microbial communities, and to what degree these mechanisms are universal, is required to for instance optimise certain medical interventions, or the way in which toxins are metabolised in the gut. With the current trend of increasing instances of antibiotic resistance, as well as modern diseases associated with lower gut diversity, it is increasingly important to map the mechanisms steering the 'social lives' of microbes in the gut.

Communications and Engagement:

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Key publications: 

van den Berg NI, Machado D, Santos S, Rocha I, Chacón J, Harcombe W, Mitri S and Patil KR. Ecological modelling approaches for predicting emergent properties in microbial communities. Nature Ecology and Evolution; 6, 855–865. (2022).

PhD Student

Contact Details

MRC Toxicology Unit
Gleeson Building
Tennis Court Road


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