DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

    More

    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

    More

    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

    More

    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

    More

    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

    More

    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

    More

    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

    More

    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

    More

    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

    More

News & Publications
Home › News Releases › A Rallying Call for Microbiome Science National Data Management

May 23, 2016

A Rallying Call for Microbiome Science National Data Management

A National Microbiome Data Center is essential for enabling exploration of all the environmental genomic data.

Massive amounts of data require infrastructure to manage and store the information in a manner than can be easily accessed for use. While technologies have scaled to allow researchers to sequence and annotate communities of microorganisms within an environment, (its “microbiome”), on an ever-increasing scale, the data management aspect has not been developed in parallel.

National Microbiome Data Center graphic

In Trends in Microbiology, DOE JGI researchers call for the formation of a National Microbiome Data Center, which complements the White House’s recent launch of a National Microbiome Initiative. (Nikos Kyrpides, DOE JGI)

In a paper published online May 16, 2016 in Trends in Microbiology, researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, call for the formation of a National Microbiome Data Center to efficiently manage the datasets accumulated globally. By integrating and harnessing all available microbiome data and metadata, researchers could conduct larger-scale comparative analyses in order to address global challenges related to energy, environment, health and agriculture.

“The time is ripe to embark on the greatest endeavor to understand Earth’s microbiome,” said Nikos Kyrpides, DOE JGI Prokaryote Super Program head and the study’s first author. “Biological sequence data should be considered an instrumental tool for the study of biology systems, analogous to the telescope for astronomy and the particle accelerator for high-energy physics.”

A Complement to the National Microbiome Initiative

The timely publication complements the White House’s launch of a National Microbiome Initiative focused on comparing microbial communities across ecosystems to identify the “organizing principles” that shape all microbiomes. A national microbiome data center, the team wrote, would “organize, process, and serve all available environmental genomic data.”

Kyrpides and his colleagues identified three bottlenecks in microbiome research associated with short-sightedness: lack of a grand vision to move beyond “single-use” microbiome datasets to a more cohesive collection; lack of interagency funding models; and, limited international data standards that hinder the global research community’s ability to efficiently conduct comparative analyses. Several large data management systems already exist to help, including the Integrated Microbial Genomes (IMG) system and the Genomes OnLine Database (GOLD) system run by DOE JGI scientists. These resources allow researchers to access and analyze publicly available assembled microbial and microbiome data and metadata, respectively. In addition, the DOE JGI has partnered with the National Energy Research Scientific Computing Center (NERSC) to operate in a high performance computing environment and support the growing community demand.

A Grand Vision as Microbiome Research Scales 

“There is a profound lack of a grand vision in appropriate funding to support the extraction of knowledge from big data (i.e., across studies),” Kyrpides said. “Furthermore, the reference data needed to contextualize the myriad microbiome samples is sorely lacking. These data are fundamental for interpretation of how microbiomes function, and how they interact within the environments and hosts they inhabit. Systematic decoding of microbes and their environments to fill in the gaps in our databases is a key step towards hypothesis-driven science and enabling a better understanding of microbial life.”

The Department of Energy has a tradition of taking on massive projects—from the first particle accelerator to its role in initiating the Human Genome Project, and the DOE JGI is no stranger to microbiome research, reporting the first genomic characterization of a microbial community back in 2004. Over the past decade, microbiome research has grown in scale, tackling projects such as termite hindgut, cow rumen, the Gulf of Mexico oil-eating microbiome, prairie soils and permafrost. Through the Community Science Program, the largest dataset focused on oxygen minimum zones and what has been described as the “only systematically and quantitatively prepared dataset available” for the viral ecology community were developed in collaboration with the DOE JGI.

“At the dawn of the third decade of microbial genomics, and well into the information age, the establishment of a national microbiome data center can pave the way to understanding the Earth’s microbiome,” Kyrpides said.

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)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases

More topics:

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

Related Content:

SPRUCE-ing Up Science

mentors and interns for JGI-UC Merced internship program

JGI at 25: Studying Sorghum’s Survival Skills

A graphic showing citations of the Sorghum bicolor reference genome

Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts

Single filament of Ca. Thiomargarita magnifica (Jean-Marie Volland)

Polar Phytoplankton Need Zinc to Cope with the Cold

Photograph of a stream of diatoms beneath Arctic sea ice.

JGI at 25: Solving the Mystery of the Missing Oil

A surface slick in the Gulf of Mexico, taken ~1.5 km from the Deepwater Horizon wellhead (Olivia Mason, LBNL).

JGI at 25: The Human Genome Project, or the JGI’s Origin Story

JGI contributions detailed in DOE Human Genome Project poster
  • 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

© 1997-2022 The Regents of the University of California