Research Interests

Understanding the dynamic processes by which microbial community metabolism transform biopolymers and metabolites within their environment.

We are interested how microbial communities are structured by the biopolymers and metabolites in their environment and the dynamic and reciprocal processes by which they transform these pools. Central to these efforts are the development of mass spectrometry approaches to study these processes including exoenzyme activity profiling, exometabolomics and mass spectrometry imaging. Together these allow us to comprehensively characterize metabolic activities, dynamics and localization within complex cellular systems to predict responses and design interventions.

Exometabolomics approach

Using mass spectrometry we can measure quantitative changes in the composition of the metabolites in the environment as a result of microbial metabolism. Our lab is using exometabolomics to define the metabolite exchange capabilities of individual community members. We are constructing lab mesocosims and using mass spectrometry to characterize the resulting interactions under controlled environmental conditions to determine the structure and dynamics of distributed microbial metabolic networks. Microscopic organisms account for the majority of biomass on earth and are responsible for elemental cycling on earth. They also account for nine out of ten cells in our bodies. Yet while microbes essentially are only found in nature as diverse microbial communities, most of what we know about them is based on laboratory studies on isolates. As part of numerous collaborations we are working to understand the coupling of cellular metabolism in microbial communities to create distributed and robust metabolic networks by using exometabolomics to characterize metabolite exchange between microbes. This understanding will be critical in understanding how to predict and manage microbial communities for long-term sustainability.

High throughput NIMS Exoenzyme Activity Analysis

Technical advances in DNA sequencing and manipulation have lead to an explosion in the sequenced universe and the ability to create libraries of millions or billions of bacterial variants. However, defining the functions of these remains slow and tedious. Our lab has a long-standing interest in nanostructure-initiator mass spectrometry (NIMS) to increase the
pace of functional genomics and synthetic biology. We are using this in conjunction with nanoliter-scale manipulation of liquids for rapid mass spectrometry functional analysis. We are particularly interested in the exoenzymes used by microorganisms to deconstruct plant and other biopolymers such that they can be uptaken into the cells. Through bioconjugate chemistry we modify these sugars enabling rapid detection and quantification using NIMS. At the Joint BioEnergy Institute, we employ this technique to help develop cellulosic biofuels both through screening metabolism and development of effective cocktails for deconstructing plant biomass.

Selected Publications

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