Systems Biology of Microbial Communities

Communities of interacting microbes are abundant in nature and play critical roles at virtually all levels of life, ranging from global carbon cycling to the formation of oral cavities.  Microbial communities can benefit us as resident microbiome, for example by facilitating food digestion or by blocking harmful pathogens.  They can also harm us, for example by causing persistent infections in slow-healing wounds or in lungs of cystic fibrosis patients.  Through interactions among species, microbial communities exhibit overall functions that cannot be achieved efficiently by any single member species.  The aim of the lab is to understand how cell-level interactions among members lead to such community-level functions.

Complexity of natural microbial communities (involving many species, multitude of interactions, and non-steady environment) has impeded attempts to discover the link between community interactions and functions.  To study microbial communities, our lab instead examines communities at different levels of complexity to search for general governing principles.  These include simulated in silico communities, synthetic communities of microbes engineered to engage in defined interactions, and simple microbial communities isolated from nature.  Taking an interdisciplinary approach, we combine quantitative experimentation with mathematical modeling to discover interactions and to explain functions that arise from those interactions.  Our long-term goal is to devise strategies to control microbial communities.  This will have broad impact in biomedical applications (e.g. managing microbial infections), environmental applications (e.g. degrading waste), as well as industrial applications (e.g. producing biofuels).