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.

De ecologie van infecties

[Dutch] Bacteriën vormen vaak een minisamenleving. Ze reageren op elkaar en op invloeden van buitenaf, zoals voedsel of antibiotica. Inzicht in de interacties tussen bacteriën is fundamenteel interessant én voor de medische praktijk. Bijvoorbeeld in het geval van blaasontstekingen. Bij ouderen worden die vaak niet door één maar door meerdere bacteriën tegelijk veroorzaakt – het zijn polymicrobiële infecties – waarbij de bacteriën bovendien verschillende antibiotica resistentieniveaus hebben.

Meer lezen over de ecology van infecties?: Uitgelicht: de ecologie van infecties

Postdoc – Predicting evolution

Join us! Or any of the other labs involved.

Six postdoc positions in Origins of Life research

The Origins Center

The Origins Center is a recent, multidisciplinary and multi-institute initiative of a large number of top tier scientists in the Netherlands, who responded to questions submitted by the public on fundamentals of life in the universe in the context of the Dutch National Science Agenda. Recently we defined the outlines of five three-year pathfinder projects that together should lay the groundwork for a future, far larger research programme which aims at game-changing understanding of the origin of life and of life-bearing planets, predicting evolution, building and steering life from molecule to biosphere, finding extra-terrestrial life and of the mathematical concepts needed for bridging large spatial, temporal and organisatorial scale differences. The Center is coordinated by the University of Groningen, the Netherlands. Scientists affiliated with at least 17 Dutch universities and research institutes participate in its research. Recently the Netherlands Organisation for Scientific Research NWO granted ‘Startimpuls’ (Initial Boost) funding to the Origins Center.

For the pathfinder projects we are now recruiting six postdoctoral research fellows with a strong background in astronomy, biophysics, chemistry, microbiology, ecology, evolutionary biology, mathematics, computational science, molecular biosciences or planetary and geosciences, and with the ability to perform innovative and multidisciplinary research. The recruited fellows will, jointly with several research groups in the Netherlands, further define and execute the projects. They will thereby be centrally involved in advanced and multidisciplinary research of great scientific and public interest.

Click here for more information on the Predicting evolution project (Pathfinder 2).



Microbial Darwinian Medicine: A Workshop at the Interface of Medicine and Microbial Eco-Evolutionary Biology

14-17 August 2017, Lorentz Center Leiden, NL

Human health is increasingly recognized to also depend on consortia of bacteria that interact with each other and the host. Bacterial communities in the gut microbiome are for example essential for nutrient absorption and protection against pathogens, and changes in the microbial associates can contribute to e.g. diabetes, obesity and antibiotic-resistant infections (such as infections of the urinary tract and the lungs of cystic fibrosis patients, and irritable bowel syndrome). Theoretical and experimental biology has been instrumental in elucidating how microbial interactions shape the stability of microbial consortia, and particularly how interventions, such as antibiotic treatment, affect their (co)existence. This is directly relevant from a medical perspective, but the application of evolutionary and genomic approaches to understand clinical systems has been limited. Darwinian medicine seeks to do just that.

Great advances in sequencing tools and bioinformatics help us to better understand which bacteria are where, how their genomes evolve over time, and how pathogens and antibiotic resistance traits are transmitted over time. However, there are many challenges in the interpretation of data and the translation of results into improved clinical tools and practices. For example, are mutations in pathogens during infection adaptations to the host-environment, or an adaptation to inter-bacterial interactions? And are ecological shifts in the microbiome the cause or effect of disease? This workshop will address the current understanding of how changes in the microbiome affect human health, and how we can move from correlative patterns to causative effects. To do so we need a joint approach, which transcends the boundaries of clinical, comparative genomic, and experimental biological fields.

This workshop will bring together a group of scientists from clinical, genomic/bioinformatic, and evolutionary biology backgrounds. Each day of the workshop has a theme, and the stage is set with a combination of longer and shorter (PechaKucha style) presentations. The speakers of the day will join subgroups of participants for in-depth discussions, followed by a plenary synthesis discussion. Rotating group compositions, poster presentations and informal socializing will facilitate the aim of furthering the interdisciplinary field of microbial Darwinian medicine.

Scientific organizers:

Sandra Breum Andersen (New York, USA)
Jesse Shapiro (Montreal, Canada)
Christina Vandenbroucke-Grauls (Amsterdam, The Netherlands)
Marjon de Vos (Wageningen, The Netherlands)

Workshop Coordinator: Martijn Fritsen, Tel: +31 71 527 5542

Workshop free of charge, selection based on relevance and motivation.

More information and registration


Ecology of infections

Past week I’ve presented some of my work on the ecology and evolution of antibiotic resistance in urinary tract infections at the 99th Dies Natalis (university’s birthday) of Wageningen University.

Therefore we recorded a clip on the problem of antibiotic resistance (in Dutch).

And you can find some more background on my research on the ecology of infections here.

You can find more background on antibiotic resistance in the Netherlands here (in Dutch).