New Lab Members

From September on we will have few new lab members.

A new PhD student will investigate the role of epistasis and ecological interactions on the evolution of antibiotic resistance and horizontal gene transfer in polymicrobial infectious communities – and MSc students will work together with the PhD students in silico and in the laboratory, online and offline.

Due to COVID-19 measures it is yet unclear when the labs will reopen –

we keep our fingers crossed for September!

PhD Scholarship Program

We are looking for talented students who wish to design their own PhD research project within the scope of the research theme Adaptive life. Please click on the following link for a non-exhaustive list of topics and associated supervisors:…)research-topics.docx.

You are expected to write your own research proposal on one of the topics related to the theme Adaptive Life. One of these topics is The spread of antimicrobial resistance via horizontal gene transfer in infectious microbial communities. Supervised by Marjon de Vos, Sander van Doorn and Oscar Kuipers. If you are interested in this topic – feel free to contact me.

You can send in your application, including a short research proposal before 1 April 2020.

More information can be found here.



Darwin can help your Doctor

Taking an evolutionary view can inspire new ideas in clinical microbiology. For example, evolutionary studies can reveal why some antimicrobial dosing regimens are better than others in preventing the development of drug resistance. Looking at microbial communities, rather than just the pathogenic micro-organisms, can also lead to new insights. That is why clinicians, bioinformaticians analysing pathogens and evolutionary biologists should all work together. Read more here.

Two new preprints

Microbial Evolutionary Medicine – from theory to clinical practice.  S Breum Andersen, BJ Shapiro, C Vandenbroucke-Grauls, MGJ de Vos. 2018, PeerJ Preprint.

Abstract. Bacteria and other microbes play a crucial role in human health and disease. Medicine and clinical microbiology have traditionally attempted to identify the etiological agents that causes disease, and how to eliminate them. Yet this traditional paradigm is becoming inadequate for dealing with a changing disease landscape. Major challenges to human health are noncommunicable chronic diseases, often driven by altered immunity and inflammation, and persistent communicable infections whose agents harbor antibiotic resistance. It is increasingly recognized that microbe-microbe interactions, as well as human-microbe interactions are important. Here, we review the “Evolutionary Medicine” framework to study how microbial communities influence human health. This approach aims to predict and manipulate microbial influences on human health by integrating ecology, evolutionary biology, microbiology, bioinformatics and clinical expertise. We focus on the potential promise of evolutionary medicine to address three key challenges: 1) detecting microbial transmission; 2) predicting antimicrobial resistance; 3) understanding microbe-microbe and human-microbe interactions in health and disease, in the context of the microbiome.

Ecology dictates evolution? About the importance of genetic and ecological constraints in adaptation. MGJ de Vos, SE Schoustra, JAGM de Visser. 2018, OSF Preprint.

Abstract. The topography of the adaptive landscape is a major determinant of the course of evolution. In this review we use the adaptive landscape metaphor to highlight the effect of ecology on evolution. We describe how ecological interactions modulate the shape of the adaptive landscape, and how this affects adaptive constraints. We focus on microbial communities as model systems.

Published in Europhysics Letters (EPL), Volume 122, Number 5 – Focus Issue Evolutionary Modeling and Experimental Evolution

Polymicrobial infections: ecosystems with special properties

We published a perspective on the ecology of polymicrobial infections in the Dutch Journal of Medicine (NTvG).

Bacteria often live together in complex communities. Insight into these microbial ecosystems is essential to make it possible to intervene when these ecosystems lead to disease. Bacteria do not only respond to their host, but they also affect each other, which may have far-reaching consequences for the course of the disease. In this article we describe that clinical isolates in a polymicrobial infection can be seen as ecosystems. These ecosystems often have properties that separate isolates do not have; they may, for example, be more virulent or more resistant to antibiotics. We therefore emphasize that the whole is greater than the sum of its parts, even for infections.