Ik gebruik experimenten om te bestuderen hoe organismen gemeenschappen vormen en hoe ze zich aanpassen tot stabiele ecosystemen. Hiervoor gebruik ik twee experimentele modelsystemen: (1) traditionele gefermenteerde producten uit Zambia, Flevoland en andere plekken op de wereld die natuurlijke microbiele gemeenschappen bevatten en (2) filamenteuze schimmels (Aspergillus fumigatus) met (on)selectieve druk van azool-fungiciden.

Hoewel mijn voornaamste interesse ligt in de studie van microbiële ecologie en evolutie met behulp van deze experimentele systemen, hebben zowel het modelsysteem van traditioneel gefermenteerd voedsel als Aspergillus fumigatus-schimmelgemeenschappen in de context van azoelresistentie veel interdisciplinaire projecten geïnitieerd.

Het werk aan traditionele fermentatie houdt verband met voedselfermentatie, menselijke voeding en gezondheid en met ondernemerschap van vrouwelijke ondernemers. Deze projecten hebben tot doel traditionele gefermenteerde voedingsmiddelen te promoten en zo voedsel- en voedingszekerheid te bevorderen.

De projecten op het gebied van Aspergillus fumigatus doe ik in samenwerking met beleidsmakers, landbouwers en artsen zodat er gezocht kan worden naar maatregelen om azoolresistentie in verschillende sectoren te verminderen. 

How organisms adapt to novel environments, as single genotypes and as complex communities, is one of the key questions in biology and central to my research. In a mix of fundamental and applied projects, my research sheds light on this basic question, and at the same time aims to develop applications addressing problems in society such as the development of indigenous knowledge and the spread of antibiotic/fungicide resistance. Central themes in my research include evolution of interaction between microbes, the dynamics of adaptation and speciation, the role of sex in evolution and the study of microbial communities within fermented products.

1. Traditional fermented foods

Ecology and evolution of natural microbial communities. Analogous to well-known fermented products such as yoghurt, wine, beer and sauerkraut, Zambia has many endogenous fermented products. The fermentation processes are ancient and result in safe products with an increased nutritional value and an increased shelf life than the raw materials. The microbiology of fermentation in these traditional foods is largely unknown and represents an outstanding opportunity for addressing both fundamental and practical questions of wide concern. For instance, why are the microbial communities in these fermented products so stable and what mechanisms prevent the invasion of novel strains such as pathogenic bacteria? Could we disentangle adaptive processes that occur at the short term (ecology – species sorting) and the longer term (evolution – fixation of novel mutations). These questions represent long-standing issues in community ecology and evolutionary biology, namely, what makes natural microbial communities both diverse and stable over the long-term.

Interdisciplinarity. In various projects I collaborate with numerous colleagues to link to aspects of food microbiology, consumer studies, human nutrition and women entrepreneurship. Not only does this broaden the scope of this work, it helps to prioritize research questions in the field of ecology and evolution. https://www.wur.nl/en/project/traditional-fermented-foods-to-promote-food-and-nutrition-security-in-africa.htm

Science for development and international collaboration. I work in close collaboration with the University of Zambia, where I hold a position. Further, collaborations with Chinhoyi University of Technology Zimbabwe, Université d’ Abomey-Calavi and connections with practitioners and their organisations help to contextualize my work and to promote science for development.

Interdisciplinarity. In various projects I collaborate with numerous colleagues to link to aspects of food microbiology, consumer studies, human nutrition and women entrepreneurship. Not only does this broaden the scope of this work, it helps to prioritize research questions in the field of ecology and evolution. https://www.wur.nl/en/project/traditional-fermented-foods-to-promote-food-and-nutrition-security-in-africa.htm

Science for development and international collaboration. I work in close collaboration with the University of Zambia, where I hold a position. Further, collaborations with Chinhoyi University of Technology Zimbabwe, Université d’ Abomey-Calavi and connections with practitioners and their organisations help to contextualize my work and to promote science for development.

Selected publications.

Schoustra SE, Kasase C, Toarta C, Kassen R, Poulain AJ. 2013. Microbial Community Structure of Three Traditional Zambian Fermented Products: Mabisi, Chibwantu and Munkoyo. PLOS ONE 8:e63948. https://doi.org/10.1371/journal.pone.0063948

Groenenboom AE, van den Heuvel J, Zwaan BJ, Smid EJ, Schoustra SE. 2022. Species dynamics in natural bacterial communities over multiple rounds of propagation. Evolutionary Applications 15:1766-1775. https://doi.org/10.1111/eva.13470

Moonga HB, Schoustra SE, van den Heuvel J, Linnemann AR, Samad MS, Shindano J, Smid EJ. 2020. Composition and diversity of natural bacterial communities in mabisi, a traditionally fermented milk. Frontiers in Microbiology 11:1816. https://doi.org/10.3389/fmicb.2020.01816

Materia VC, Linnemann AR, Smid EJ, Schoustra SE. 2021. Contribution of traditional fermented foods to food systems transformation: value addition and inclusive entrepreneurship. Food Security doi:10.1007/s12571-021-01185-5.

2. Environmental selection of azole resistance in Aspergillus fumigatus communities

Evolution of azole resistance in Aspergillus communities. Decaying organic material (compost) contains microbial communities consisting of fungi and bacteria. Here, I focus on fungal communities of Aspergillus fumigatus and their evolution towards resistance to fungicides (azoles). There is evidence that the specific community dynamics that involves long-term exposure to azoles, resistance mutations followed by sexual reproduction to recombine various resistance mutations leads to persistent high resistance to both agricultural fungicides as well as medical drugs used to treat patients suffering from fungal infections. Research questions focus on evolution to resistance in the environment, cross resistance to medical drugs, mutational effects, evolution of community structure and the role of sex and recombination to speed up adaptation.  

https://www.wur.nl/en/project/one-health-consequences-of-circularity.htm

Societal relevance, policy and measures. Environmental selection for azole resistance causes cross- resistance to medical azoles and a public health problem. Informed by policy makers, farmers, processors of plant waste and various practitioners, I have worked on the identification of hotspots and coldspots in the environment for azole resistance development. This work has been published in reports of the RIVM and has been presented to the Dutch National Parliament (Tweede Kamer).

Selected publications.

Schoustra SE, Debets AJM, Rijs AJ, Zhang J, Snelders E, Leendertse PC, Melchers WJ, Rietveld AG, Zwaan BJ, Verweij PE. 2019. Environmental Hotspots for Azole Resistance Selection of Aspergillus fumigatus, the Netherlands. Emerging Infectious Disease journal 25. 10.3201/eid2507.181625

Zhang J, Lopez Jimenez L, Snelders E, Debets AJM, Rietveld AG, Zwaan BJ, Verweij PE, Schoustra SE. 2021. Dynamics of Aspergillus fumigatus in Azole Fungicide-Containing Plant Waste in the Netherlands (2016-2017). Appl Environ Microbiol 87. 10.1128/AEM.02295-20

Zhang J, van den Heuvel J, Debets AJM, Verweij PE, Melchers WJG, Zwaan BJ, Schoustra SE. 2017. Evolution of cross-resistance to medical triazoles in Aspergillus fumigatus through selection pressure of environmental fungicides. Proceedings of the Royal Society B: Biological Sciences 284. 10.1098/rspb.2017.0635

Schoustra SE, Zhang J, Zwaan BJ, Debets AJM, Verweij PE, Buijtenhuijs D, Rietveld AG. 2019. New insights in the development of azole-resistance in Aspergillus fumigatus.  RIVM, Utrecht. RIVM Letter Report 2018-0131;  https://www.tweedekamer.nl/kamerstukken/brieven_regering/detail?id=2019Z20378&did=2019D42537  

List of projects

Project summaries

INREF traditional fermented foods to promote food and nutrition security

Aspergillus fumigatus work on environmental selection of azole resistance

Specific projects

Antifungal resistance in Aspergillus fumigatus and air sampling

Eco evolutionary dynamics in natural and laboratory ecosystems

Elimination of toxin producing fungi by competitive exclusion, the case of maize production chain in Zambia

Experimental tests of niche exclusion principle

Microbial ecology and evolution principles in mursik

Antifungal resistance development in a human pathogenic fungus

Community functionality linked to species diversity

Dynamics of microbial comminates in traditional fermentation in natural environments

Diversity, evolution and function in microbial communities

Evolutionary ecology of microbiome structure and functionality in anthropogenically engineered ecosystems

Effect of traditional fermented food intake on gut microbiota among children

Linking species composition to overall ecosystem functioning

Upgrading of traditional processing of Mahewu in Zimbabwe

Upscaling of Akpan processing in Benin

GEN11806 Principles of Genetics

GEN21803 Principles of Human Genetics

FHM30806 Advanced Fermentation Science

HNH39806 Micronutrient Deficiencies in Low and Middle Income Countries