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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.”

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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    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.

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Home › Our Science › Science Programs & Platforms Leads › Microbiome Data Science Group

Microbiome Data Science Group

Research in Kyrpides group focuses on Microbiome Data Science and analysis of Big Data.

Biology is currently experiencing a revolution brought on by rapid developments in genomics and other omics technologies. The exponential growth of DNA sequencing data, coupled with recent computational technology advances in management, processing and visualization of “big data,” and artificial Intelligent/machine learning approaches in data analysis and interpretation is creating new opportunities for breakthrough discoveries and catalyzing a major transition of biology into data science.

The research efforts of the group have concentrated in demonstrating the power of data science in tackling grand challenges in Biology, with a special focus on microbiome research.  These efforts include exploration of the global diversity of alternative genetic codes (Science 2014), unearthing hundreds of thousands of new viral genomes and their predicted hosts (Nature 2016, Science 2017, Nature Microbiology 2018), discovery of new genes with important biotechnological applications (e.g., new CRISPR-Cas variants and new CRISPR-Cas types) (Nature Communications 2017, Science 2018, Molecular Cell 2019) and massive reconstruction of genomes from uncultivated microbes (Nature 2019).

Other projects in the group include the sequencing and comparative analysis of thousands of archaeal and bacterial type strains (GEBA-type strains project), the delineation of host-virus interactions, the exploration of the functional dark matter as well as the development of novel methods to enable large-scale comparative analysis, mining and visualization of big data.

Research Team

      Nikos Kyrpides,       PI     Stephen Nayfach,
Research Scientist
 Antonio Camargo,
Project Scientist
Russell Y. Neches,
Postdoctoral Fellow
Brayon J Fremin
Postdoctoral Fellow
Lee Call,
Postdoctoral Fellow
nckyrpides@lbl.gov
(925) 296-5718
snayfach@lbl.gov
(925) 296-5848
antoniop.camargo@lbl.gov   ryneches@lbl.gov   bfremin@lbl.gov     lcall@lbl.gov

More about Nikos

Stephen’s research is focusing on population genomics and on the development of computational methods for large scale reconstruction of genomes from metagenomes

Stephen’s GitHub

Antonio’s research is focusing on the development of new methods for the identification of viral sequences from metagenomic data

Russell’s research  focuses on the analysis of soil virome and the development of novel approaches to enable biogeographic analysis of big data.

Meet Russell

Russell’s GitHub

Brayon’s research is focusing on the identification of small proteins, structural RNAs and RNA viruses from metagenomic data

Lee’s research  focuses on large scale microbiome and virome data analysis

 

Selected-Publications

  1. Nayfach S, et al. (2021) CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nature Biotechnol. Epub.
  2. Nayfach S, et al. (2021) A genomic catalog of Earth’s microbiomes. Nature Biotechnol. 39(4):499-509.
  3. Almeida A, et al. (2020) A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnol. 39(1):105-114.
  4. Schulz F, et al. (2020) Giant virus diversity and host interactions through global metagenomics. Nature 578(7795):432-436
  5. Sberro H, et al. (2019) Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes.. Cell 178(5):1245-1259
  6. Nayfach S, et al, (2019) New insights from uncultivated genomes of the global human gut microbiome. Nature  568(7753):505-510
  7. Amann R. et al (2019) Toward unrestricted use of public genomic data. Science  363(6425):350-352
  8. Harrington LB, et al (2018) Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science 362(6416):839-842.
  9. Duerkop BA, et al. (2018) Murine colitis reveals a disease-associated bacteriophage community. Nat Microbiol. 3(9):1023-1031
  10. Harrington LB et al. (2017) A thermostable Cas9 with increased lifetime in human plasma. Nat Commun. 8(1):1424.
  11. Sczyrba A, et al. (2017) Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nature Methods 14(11):1063-1071
  12. Bowers RM, et al. (2017) Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology 35(8):725-731
  13. Paez-Espino D. et al. (2017) Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. Nature Protoc. 12(8):1673-1682
  14. Mukherjee S, et al. (2017) 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nature Biotechnology 35(7):676-683
  15. Schulz F, et al. (2017) Giant viruses with an expanded complement of translation system components.  Science  356: 82-85
  16. Ovchinnikov S. et al. (2017) Protein structure determination using metagenome sequence data. Science 355(6322):294-298
  17. Paez-Espino D. et al. (2017) IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 45(D1):D457-D465.
  18. Chen IA et al. (2017) IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 45(D1):D507-D516
  19. Paez-Espino, D. et al. (2016) Uncovering Earth’s virome. Nature 536:425-30
  20. Kyrpides NC. et al. (2016) Microbiome Data Science: Understanding Our Microbial Planet. Trends Microbiol. 24(6):425-7.
  21. Eloe-Fadrosh EA, et al. (2016) Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nature Microbiol. 15032
  22. Eloe-Fadrosh EA, et al. (2016) Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs. Nature Commun. 7:10476
  23. Varghese NJ, et al. (2015) Microbial species delineation using whole genome sequences. Nucleic Acids Res. 43(14):6761-71
  24. Kyrpides NC et al. (2014) Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains. PLoS Biology 12(8):e1001920
  25. Ivanova N. et al. (2014) Stop Codon Reassignments in the Wild. Science 344(6186):909-13
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