DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    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.

    More

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

    More

    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.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    A panoramic view of a lake reflecting a granite mountain.
    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.

    Listen

    A light green shrub with spiny leaves, up close.
    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.

    Listen

    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    iPHoP image (Simon Roux)
    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.

    More

    Abstract image of gold lights and squares against a black backdrop
    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.

    More

    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.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    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.

    More

    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.

    More

    croppe image of the JGI helix sculpture
    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.

    Listen

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    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.

    More

    image from gif that shows where in the globe JGI fungal collaborators are located.
    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.

    More

    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.

    More

Our Science
Home › Science Highlights › First Public Resource for Secondary Metabolites Searches

August 5, 2015

First Public Resource for Secondary Metabolites Searches

IMG-ABC allows researchers to link sequencing data and the search for novel biosynthetic gene pathways.

A chart of ecosystem sources for the 10 most common biosynthetic cluster enzymatic types. Generating these data in the IMG-ABC database is made possible by the integration of the portal with the IMG and GOLD databases, which allow access to metadata annotations. (Credit: Hadjithomas M et al. mBio Jul 2015)

A chart of ecosystem sources for the 10 most common biosynthetic cluster enzymatic types. Generating these data in the IMG-ABC database is made possible by the integration of the portal with the IMG and GOLD databases, which allow access to metadata annotations. (Credit: Hadjithomas M et al. doi: 10.1128/mBio.00932-15 through CC BY-NC-SA 3.0 license.)

The Science:

The wealth of genomic and metagenomic datasets for microbes, particularly from previously unstudied environments, within the Integrated Microbial Genomes (IMG) system is being applied in a new public database to the search for novel secondary metabolites that could be used in a wide range of applications from bioenergy to health.

The Impact:

This public database allows researchers to more efficiently harness the genomic data generated by advanced sequencing technologies to identify novel small molecules relevant to DOE missions in bioenergy and environment.

Summary

Secondary metabolites are organic compounds that aren’t involved in functions such as growth or reproduction but which may still play key roles in regulation, immunity, or other vital pathways in an organism. Many secondary metabolites from plants and microbes also have been shown to have commercial applications; for example, terpenes from a variety of plants including eucalyptus have bioenergy applications.

In a study published July 14, 2015 in mBio, researchers from the DOE Joint Genome Institute, a DOE Office of Science User Facility, the Biosciences Computing Group at Lawrence Berkeley National Laboratory, and the University of California, San Francisco, describe a new public database that allows researchers to search for biosynthetic gene clusters and secondary metabolites. The database is known as IMG-ABC because it is an Atlas of Biosynthetic gene Clusters within the Integrated Microbial Genomes (IMG) system and includes information from single-cell and metagenome data from the DOE JGI’s Microbial Dark Matter project.

“For the first time,” the team reported, “IMG-ABC links information regarding genomic pathways for the biosynthesis of secondary metabolites with chemical structure information on a scale of several thousand data sets. With careful efforts for quality control, it combines the predictive power of state-of-the-art computational tools… with the exhaustive analysis framework offered by the IMG family of systems. This combination delivers a powerful punch, predicting both familiar and novel biosynthetic gene pathways in thousands of cultured isolates, single cells, and metagenomes.”

The team conducted a pilot “proof-of-principle” study in which they searched through more than 25,000 isolate microbial genomes for biosynthetic clusters that contain at least six of the seven core genes required to produce phenazine, a compound that acts as a shuttle for electrons in metabolism, is found in bacteria that can process nutrients from wastes, and from which dyes and antibiotics are also derived. The search yielded nearly 1,000 hits and identified potentially novel phenazine pathways in Gammaproteobacteria, Betaproteobacteria, and Actinobacteria, and even, unexpectedly, in a root-nodulating bacterium.

Processing vast amounts of genomic and metagenomic data requires a high performance computing environment, and in this case, the DOE JGI relies on high-efficiency resources from the National Energy Research Scientific Computing Center (NERSC) to support the demand for computational access.

DOE JGI Prokaryote Super Program head Nikos Kyrpides alluded to the development of IMG-ABC when he discussed future plans for the continuing improvement of the IMG database on its 10th anniversary. “There’s a huge amount of functionality in IMG already, but we certainly need to continue adding more,” he said. “The two main directions in the near future include adding more functionality and efficient supporting data/size growth.”

Contact

Nikos Kyrpides
DOE Joint Genome Institute
nckyrpides@lbl.gov

Funding

  • U.S. Department of Energy Office of Science
  • University of California
  • Howard Hughes Medical Institute

Publication

Hadjithomas M et al. IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites. mBio. 2015 Jul 14;6(4). pii: e00932-15. doi: 10.1128/mBio.00932-15.

Related Links

  • http://jgi.doe.gov/enhancing-ecoli-pathways-for-biofuel-production/
  • http://genome.jgi.doe.gov/MDM/MDM.home.html
  • http://jgi.doe.gov/boldly-illuminating-biologys-dark-matter/
  • http://jgi.doe.gov/data-quality-data-sets-and-new-directions-plotting-img-next-10-years/
  • http://www.nersc.gov/

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

Filed Under: Science Highlights

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

You can move, but you can’t hide

Illustration of a magnifying glass identifying viruses and plasmids.

iPHoP: A Matchmaker for Phages and their Hosts

iPHoP image (Simon Roux)

Supercharging SIP in the Fungal Hyphosphere

Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.

New Research Sheds Light on Diversity in the Deep Sea

A photo taken in the deep sea. Black clouds billow out of hydrothermal vents.

Sequencing Sphagnum Leads to Discovery of Sex Chromosomes

A photo of two sphagnum species: S. divinum (red) and S. angustifolium (green)]

Busting the Unbreakable Lignin

Pictured is a micrograph of Neocallimastix californiae.
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California