Genomics Research in Ecology & Evolution in Nature

The group investigates ecological and evolutionary processes in (infectious) microbial communities. We aim to understand the genotype-phenotype-fitness relationships within (evolving) communities. Additionally, we investigate the effect of microbial interactions on the evolution of antibiotic resistance. We study these eco-evolutionary processes using molecular biological tools, by performing phenotypic and growth measurements, and modelling. We currently focus on bacterial isolates from persons suffering from urinary tract infections as a model system. Additionally, we investigate the interactions between pathogens and benign bacteria discovered in the urinary tract of healthy persons. By unveiling the fundamental ecological and evolutionary microbial processes in infectious disease, we hope to improve and contribute to strategies that can alleviate infectious diseases and limit the spread of antibiotic resistance.

In my group we use ecological and evolutionary theory to unravel the causes and the consequences of free-living and host-associated microbial communities. On the one hand we are interested in understanding how microbiomes are formed (causes of microbial diversity) and what processes (stochastic determinism) and mechanisms (selection though competition or environmental filtering, dispersal, drift, speciation) lead to the development of microbial communities. On the other hand I am interested in determining what are the consequences of this microbial diversity for the functioning of the environment the microbiome is associated with – being that a host or a soil – and understanding the mechanisms determining the diversity effect. We address these topics in a range of environments (agricultural soil, salt marshes soils) and hosts (plants, arthropods, birds, mice and humans), by combining experimental procedures (field, microcosm, mesocosm, manipulative experiments), modelling, microbiological and molecular techniques, metagenomic and bioinfomatic approaches.

We strive to unravel the mechanism underlying the immense diversity of life. How do organisms adapt, differentiate and diversify? How do they shape and are shaped by the communities and ecosystems they occur in? To do so, we study a wide array of organisms and systems – from exotic viruses to their unicellular eukaryotic hosts, from endophytic fungi to carnivorous plants, and from open-ocean cyanobacteria to coastal soil microbiomes. Our focus lies in understanding processes that drive and accelerate evolution in these systems, such as horizontal gene transfer via mobile genetic elements, viruses or vesicles.

For our research, we harness the power of genomics and big data, leveraging cutting-edge sequencing technologies and devising workflows and software to maximize their use. Moreover, we are developing tools for data exploration, integration and interpretation with a focus on genomics data visualization. Combining these efforts, we aim to gain new insights into the concert of ecology and evolution that brings forth the wondrous living world around us.