Metabolomics Program

The Metabolomics Program is focused on understanding the critical roles of metabolites in living systems, particularly as they relate to DOE missions in the bioeconomy, sustainability, and environmental research. This program integrates cutting-edge metabolomics with genomic data to gain insights into how small molecules function within plants, microbes, and ecosystems. Identifying and analyzing primary and secondary metabolites helps uncover their roles in processes such as nutrient cycling, plant-microbe interactions, and environmental responses.

The program employs advanced mass spectrometry-based methods to analyze metabolites from a wide range of biological and environmental samples — including microbes, fungi, plants and soils. Through a combination of experimental workflows and computational analysis, JGI scientists are able to link metabolic activity with gene expression, providing deeper insights into functional genomics. A key focus is understanding the interactions between  plants, microbes, and soils relevant to key environmental processes and the bioeconomy including understanding enzymatic transformations, pathways, and how changes in metabolism can affect ecosystem functions.

The Metabolomics Program focuses on advancing tools and technologies to analyze metabolites in environmental organisms, communities, and samples including state-of-the-art instrumentation and informatic approaches.By bridging genomics with metabolomics, the Metabolomics Program is providing essential tools for exploring the molecular basis of complex biological systems, driving innovations in sustainable agriculture, environmental health, and bioenergy development.

• EcoFABs: For studying microbe-host (or plant-microbiome) interactions under controlled conditions, microcosms can be designed and studied in EcoFABs as a synthetic microbiome.  Here, a controlled environment of plant, microbes, fungi, etc may be established and subject to repeatable, controlled experimental manipulations while being simultaneously imaged and sampled.  Combining collected metabolomics data with genomics, transcriptomics, imaging, and other data from EcoFAB systems can provide novel insights into the impact of microbial symbionts and their hosts on ecosystems.  

• Environmental molecular network: ENVnet  is a comprehensive, mass spectrometry-based molecular network of metabolites designed to demystify the complexity of dissolved organic matter (DOM) across a variety of environments. ENVnet allows us to uncover globally distributed molecules with conserved structures, offering fresh insights into DOM's composition. With ENVnet, researchers are able to test hypotheses concerning specific molecular structures involved in DOM cycling. ENVnet can be used in your custom Python applications but highly recommend using the workflow in GNPS2.