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How do microbes interact through chemistry?

Microbes compete and cooperate through small molecules. We study this chemical crosstalk within microbial communities and between microbes and their hosts, spanning polymicrobial infection, the gut microbiome, and the discovery of new natural products from soil and cave microbes.

What is chemical ecology?

Diagram: drugs, invading pathogens and the host each act on a microbial community, which responds by producing new metabolites

Chemical ecology examines how organisms interact with one another and with their environment through chemistry. Microbes sense and respond to their surroundings by producing and detecting small molecules. We characterize how microbial communities alter their metabolic output in response to pathogen invasion, drug exposure, and changes in host physiology.

What do we do?

Research approach: define the ecological question, rebuild the microbial community and identify metabolites, then test hypotheses to establish molecular function

Our research begins with ecological questions. How do microbial communities respond when drugs, pathogens, or host factors perturb their environment, and which metabolites mediate those responses? To address them, we reconstruct communities from infection sites, the gut, and environmental sources such as soil and caves; identify candidate metabolites; and test hypotheses about their biological function. This approach informs both the biology of microbial communities and the discovery of new bioactive natural products.

How do we test hypotheses?

Hypothesis testing approaches: genetics (gene deletion and complementation), biochemistry (heterologous expression), co-culture with microbes and host cells, and phenotypes (virulence, fitness, tolerance, cytotoxicity); metabolomics and molecular networking identify candidate metabolites

We define the function of microbial metabolites using genetic, biochemical, and cell-based approaches, including targeted gene deletion and complementation, heterologous expression and enzyme characterization, defined co-culture and host cell models, and phenotypic assays of virulence, fitness, antimicrobial tolerance, and cytotoxicity. 

 

Our research is supported by the National Institutes of Health (R35GM158024). 

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