Research
We are interested in understanding the principles governing the structure and function of microbial communities. Uncovering these principles will help us rationally engineer communities to advance sustainability or human health.
Below is a glimpse of questions and projects we are currently working on.
Predicting community assembly by understanding metabolic evolution
Traits such as growth or metabolite exchange rates govern how microbes use and share resources, and are thus a key determinant of species interactions. However, predicting these quantitative metabolic traits from genomes currently remains a major challenge.
One of the main goals of our group is to understand the evolution of quantitative metabolic traits and their mapping onto genotypes. This will help us predict what genomic features determine the successful establishment of a microbe in a community, paving the way to predicting the assembly of microbiomes and their response to environmental changes.
[Science 2018] [Cell Systems 2022] [bioRxiv 2022]
Predicting the function of microbial communities
Microbial communities can perform a wide range of services, and promise new sustainable solutions across biotechnology, agriculture, or human health. In order to harness these services, we need to lear how to predict the function that a community will have based on its composition.
To accomplish this task, we recently extended the theory of fitness landscapes to characterize how the collective function of a community maps to its composition - the ecological structure-function map. We are currently exploring the properties of this map, and how it can help us engineer microbial communities.
[Plos Biology, 2019] [Nature Communications, 2021] [bioRxiv, 2022] [bioRxiv, 2022] [arXiv, 2022]
Developing computational tools to simulate microbial ecosystems
We develop state of the art computational tools to simulate microbial communities and ecosystems. We are part of the developer team of COMETS, a software platform for the “Computation of microbial ecosystems in time and space”
e-COMM: Understanding and engineering electrosynthetic communities
As part of the Zero Emission Biotechnology Program at TU Delft, we are steering our expertise to study biofilm microbial communities transforming green electricity and CO2 to valuable products. This project is a collaboration with the groups of Ludovic Jourdin and Jean-Marc Daran in our department.
© Image courtesy of Marika Zegers.
Using metabolic models to understand ecology and evolution.
We are also interested in a wide range of topics in ecology and evolution. For instance, we collaborate with Sotaro Takano (AIST, Japan) to study the evolution of metabolic strategies in microbes. We also collaborate with Maria Rebolleda-Gómez to study macroevolutionary dynamics and innovation in microbial metabolism.
For these projects, our approach is to use metabolic models, which are a great tool to explore empirically calibrated, realistic genotype-phenotype maps.
[Current Opinion in Biotechnology 2021] [Frontiers in Microbiology 2021]