Model Communities Lab · Industrial Microbiology · TU Delft

How does the architecture of living systems shape their ecology and evolution?

We build models that predictively link the architecture of complex living systems to their emergent function. For example, we ask how metabolic networks shape an organism’s phenotype, its evolution and its ecology, or how microbial interaction networks shape ecosystem function. We combine theory and computation with experiments in simple model communities. Increasingly, we take these models to real-world microbiomes in agriculture, bioremediation and industrial fermentation.

Our research Join the lab

Network

Organism

Community

Function

A metabolic network with one pathway highlighted — Networks Nonrandom architecture dictates microbial evolution and ecology.

Epistasis: the effect of species B depends on its background — Epistasis The effect of genes, but also species, depends on their interactions.

Stacked function landscapes over a network of genotypes or communities — Landscapes Smooth maps make complex functions predictable

Research program

Some questions we are trying to answer

Theory

Fitness landscapes, global epistasis and consumer–resource models: coarse-grained descriptions with predictive power across scales.

Models

We use empirically calibrated models, from mechanistic genome-scale models of single species to functional landscapes of complex communities.

Experiments

We conduct high-throughput assembly of synthetic model communities, and quantitatively dissect their physiology in bioreactors.

Selected work

Recent findings

All publications

mSystems · 2026

Integrated multi-omics and metabolic modeling links structure to function in high-performing electrosynthetic biofilm communities

Multi-omics and community metabolic models link composition to function in biofilms that convert CO₂ and electricity into acetate, butyrate and caproate.