Microbial Ecology Lab

The challenge

As humans, we are not alone: our bodies host trillions of microbes, collectively known as the microbiome. The microbiome has a major impact on human health and disease, as decades of scientific research have shown. However, we still understand only in limited detail how microbes interact with each other and with host cells, and how the behavior of individual bacteria gives rise to community-level properties. A central challenge is to connect different biological scales: from bacterial growth, metabolism, and stress responses, to ecological interactions within microbial communities, and finally to communication with the host. Our lab addresses this challenge using simplified microbial systems in the laboratory, where we can measure bacterial behavior quantitatively and test mechanistic models.

Main research areas

Studying physiology to understand ecological interactions

Bacteria such as Escherichia coli follow general physiological principles that link growth rate, cell size, gene expression, metabolism, and proteome allocation. These principles have greatly improved our understanding of how bacterial cells respond to nutrients, stress, and antibiotics. However, most of this knowledge comes from isogenic populations growing in controlled, steady, and well-mixed environments.

Our lab asks how bacterial physiology changes when cells live in more realistic ecological contexts, where they experience spatial structure, fluctuating environments, nutrient limitation, stresses, and interactions with other cells. In turn, we are interested in how physiological constraints shape ecological interactions such as cross-feeding, competition, cooperation, and antibiotic responses.

Colonization resistance, spatial structure, and rare-cell behavior

A major question in microbiome research is how resident microbial communities prevent invading species, including pathogens, from establishing themselves. This phenomenon, known as colonization resistance, depends on competition for nutrients, chemical inhibition, spatial organization, and the physiological state of both resident and invading cells.

Our group studies colonization resistance using simplified microbial communities that allow us to connect single-cell behavior to community-level outcomes. We are especially interested in situations where the fate of a population may depend on a minority of cells: for example, cells that survive stress, occupy favorable spatial positions, exploit local nutrient gradients, or initiate new patterns of growth. By following bacterial populations over space and time, we aim to understand how local interactions and spatiotemporal patterns influence coexistence, exclusion, and invasion.

Bile acids, microbial metabolism, and host communication

Microbes do not only interact with each other: they also communicate with the host by transforming molecules in the gut environment. One major focus of our lab is to understand how bacterial metabolism of bile acids shapes gut microbial ecology and host responses. Bile acids are host-derived molecules that regulate digestion, microbial growth, immune signaling, and epithelial physiology. At the same time, gut bacteria can chemically modify bile acids, changing their biological activity.

Supported by a FIS 2 grant awarded in 2025, our group studies how bacterial transformations of bile acids influence microbial community organization and host communication. We combine microbial physiology, ecology, metabolite measurements, quantitative modeling, and host-relevant assays to understand how bacterial activity reshapes the chemical dialogue between the microbiome and the host.