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    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.

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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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    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.

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    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.

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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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    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.

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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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    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.

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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 › Metagenome Program

Metagenome Program

Thermophilic microbial mat in West Thumb Geyser Basin, Yellowstone National Park (Marissa Fessenden).

Thermophilic microbial mat in West Thumb Geyser Basin, Yellowstone National Park (Marissa Fessenden).

The Metagenome Program leverages high-throughput sequencing technologies to uncover the principles governing microbial community functions and interactions that impact ecosystem processes. Sequencing technologies have allowed us to begin decoding the information encoded in the DNA of microbes in the wild, providing a snapshot of diversity and metabolic functional potential. Knowledge of how microbes function in their environment holds tremendous potential to transform our understanding of the world and spur innovations in energy and the environment.

Among the major initiatives of the Metagenome Program are:

  • Exploration of phylogenomic novelty. Advances in metagenomic sequencing, assembly, and binning have enabled reconstruction of complete or near-complete population genomes directly from the environment. These advances have led to groundbreaking discoveries in diversity and novel functions identified in unexpected microbial clades. We leverage genome-resolved metagenomics and targeted gene searches to expand representation of uncultivated microbial lineages.
  • Charting viral ‘dark matter.’ Viruses are the most abundant entities in the biosphere, and impact microbial population dynamics, long-term evolution, and ecosystem functions. Sequencing technologies have massively expanded knowledge of viral diversity and have enabled exploration of distribution and ecology at a global scale. We develop computational resources to analyze viral fragments derived from metagenomic data through IMG/VR, as well as new methods to capture viral populations from the environment.
  • Enabling microbiome data science. The microbiome research field is increasingly moving towards a data-driven enterprise, where we can begin to translate large-scale sequence data into biological insight. We enable analysis for community profiling using targeted amplicon sequencing (16S, 18S and ITS) through the iTagger pipeline and comparative genomics and metagenomics analysis through the IMG/M platform. The newly launched JGI-NERSC FICUS additionally supports users to perform state-of-the-art computational genomics and metagenomics research.

 

  • Computational systems and methods

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  • More about this program

    • Metagenomics Program Lead
  • Plant Program
  • Fungal & Algal Program
  • Metagenome Program
    • Phylogenomic Novelty
    • Viral Discovery
    • Metagenome Publications
  • Microbial Program
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  • Metabolomics Program
  • Secondary Metabolites

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