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    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

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    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

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    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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Our Science
Home › Our Science › Science Programs › Metabolomics Program

Metabolomics Program

Technical advances in DNA sequencing and related technologies has led to an explosion in the sequenced universe. However, functional characterization of these remains a difficult challenge. The Metabolomics group at JGI strives to integrate metabolomics with genomic information to provide successful functional annotation of genomes and improved understanding of the role of small molecules in diverse biological systems relevant to DOE missions.

This capability can lead to important findings:

  • Discovery of new secondary metabolites and pathways
  • Role of primary and secondary metabolites in modulating biological interactions
  • Linking environmental change with metabolism and genomics
  • Linking metabolite production and gene expression
  • Novel insights related to nutrient exchange and cross-feeding between plants, microbes, fungi and the environment
  • Microbiome nutrient cycling in soils and the rhizosphere

To analyze metabolites in complex biological systems, the Metabolomics group at JGI applies advanced mass spectrometry-based methods in combination with advanced computational analysis.  Major efforts have been made in developing workflows for extracting and profiling metabolites from a wide range of samples, including organisms (e.g. microbes, fungi, plant) and media in which they grow, as well as different types of environmental samples (e.g. soil, lake).

Using high resolution mass spectrometry coupled to liquid chromatographic separation, we are able to identify a wide range of metabolites based on thousands of metabolite standards. The following types of mass spectrometry analyses may be requested in a proposal:

  1. Polar metabolite analysis (e.g. amino acids, nucleic acids, sugars, small organic acids, metabolites in central metabolism, etc.)
  2. Non-polar metabolite analysis (e.g. secondary metabolites, polyketides, other more hydrophobic compounds, etc.)

For these analyses, JGI has run 1000+ metabolite standards (and growing) of primary and secondary metabolites including a broad range of amino acids, nucleic acids, lipids, flavonoids, alkaloids and more. These are used in our “targeted” approach, in which metabolites are definitively identified in samples based on MS properties such as retention time, fragmentation spectra and accurate mass. Our “untargeted” approach is required in the absence of standards and for discovery of novel compounds where we apply custom and open-source software and algorithms for identification.

Novel biological insights can be discovered with detected metabolites by providing an orthogonal source of information synergistic with transcriptomic and genomic datasets.  Additional capabilities in various stages of development include stable isotope labeling as well as lipidomics.  Please contact the Metabolomics group lead Trent Northen or Katherine Louie to discuss available metabolomics analyses complementary to your research.

JGI’s metabolomics capabilities can be accessed for projects that integrate with JGI’s sequencing and synthesis resources through Community Science Program (CSP) and Facilities Integrating Collaborations for User Science (FICUS) proposals. Project proposals are chosen based on scientific merit and relevance to the DOE mission, and judged through independent peer review. 

  • Resources for JGI metabolomics technology

    • Metabolite Analyses
    • Metabolite Standards in JGI Library
    • Metabolomics Results – Basic
    • Metabolomics Instrumentation
    • Sample Submission and Guidelines
    • Metabolomics Select Publications
  • More about this program

    • Metabolomics Technology Lead
  • Plant Program
  • Fungal & Algal Program
  • Metagenome Program
  • Microbial Program
  • DNA Synthesis Science Program
  • Metabolomics Program
    • Metabolite Analyses
    • Metabolite Standards in JGI Library
    • Metabolomics Results - Basic
    • Metabolomics Instrumentation
    • Sample Submission and Guidelines
    • Metabolomics Select Publications
    • Metabolomics Data Analysis - Tips From Users
  • Secondary Metabolites

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