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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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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 Group:
    • 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

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