DOE Joint Genome Institute
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Scientists at JGI
Tracking Microbial Succession in Petroleum Wells
While shifting toward more sustainable, alternative energy sources, people still rely on fossil fuels for energy and transportation fuels. Understanding how microbial communities in subsurface petroleum reservoirs are impacted by human activity, and how their responses can sour oil production, can influence oil industry practices.
Insights into A Eukaryotic Alga
Through the DOE JGI's Community Science Program, a 50-member team led by University of Maine, Carnegie Institution for Science, and East Carolina University researchers sequenced and analyzed the genome of the red alga Porphyra umbilicalis.
New Technology to Access Microbial Dark Matter
Enabled by the DOE JGI's Emerging Technology Opportunity Program, Stanford researchers extracted 29 novel microbial genomes from Yellowstone hot spring samples while still preserving single-cell resolution to enable accurate analysis of genome function and abundance.
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Approved User Proposals
Developing an Ice Plant Gene Atlas
The ice plant was the first reported halophytic, facultative crassulacean acid metabolism (CAM) species, meaning that the plant can be induced to switch from C3 photosynthesis to CAM following water-deficit or salinity stress treatment.
Exploring Deep Biosphere Microbial Communities
The data from one of the least understood habitats on Earth will have implications for our understanding of global energy and nutrient cycles, the potential for deep terrestrial disposal of nuclear waste and geo-engineering for CO
storage, while also providing insights about how life could be sustained on other planets.
A Suillus Genus Genome Atlas
As symbiotic ectomycorrhizal fungi (EMF),
spp. play critical roles in the function of forest ecosystems by providing their plant hosts with mineral resources in exchange for photosynthetically fixed carbon.
Data & Tools
DOE JGI Database of DNA viruses and retroviruses debuts on IMG platform
In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit the global community of microbial researchers.
Benchmark Study for Improving Microbial Community Profiling
Researchers used synthetic and natural microbial lake communities to compare the microbial community profiles generated from high throughput short-read sequencing and high throughput long-read sequencing approaches.
Better Microbial Genome Binning with MetaBAT
An automated tool called MetaBAT that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes.
Read more about MetaBAT
User Program Info
Community Science Program (CSP)
Submit a Proposal
Meet a JGI User: C. Titus Brown
"JGI is one of the only places that invests systematically and heavily in non-biomedical sequencing. This has tremendously enriched our knowledge of everything from microbes involved in biogeochemical cycling to organisms that are very evolutionarily distant."
DOE User Facilities Partner for Greater Scientific Impact
A total of 14 proposals were selected from a joint JGI-EMSL call for 2018 research under the Facilities Integrating Collaborations for User Science (FICUS) initiative. This is the This was the fifth FICUS call between EMSL and JGI since the collaborative science initiative was formed in 2014.
DOE User Facilities Join Forces to Tackle Biology’s Big Data
Six proposals have been selected to participate in a new partnership between the DOE JGI and the National Energy Research Scientific Computing Center (NERSC) - two U.S. Department of Energy (DOE) user facilities at Berkeley Lab.
News & Publications
Defining Standards for Genomes from Uncultivated Microorganisms
An international team led by DOE JGI researchers has developed standards for the minimum metadata to be supplied with single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) submitted to public databases.
Uncovered: 1000 New Microbial Genomes
DOE JGI scientists have taken a decisive step forward in uncovering the planet’s microbial diversity, reporting the release of 1,003 phylogenetically diverse bacterial and archaeal reference genomes—the single largest release to date—in Nature Biotechnology.
Fungal Enzymes Team Up to More Efficiently Break Down Cellulose
In Nature Microbiology, a team led by researchers at UC Santa Barbara has found for the first time that early lineages of fungi can form complexes of enzymes capable of degrading plant biomass. The work was enabled by harnessing the capabilities of two U.S. Department of Energy (DOE) Office of Science User Facilities: the DOE JGI and EMSL.