Nikos Kyrpides: The Microbial Earth Project

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Nikos Kyrpides talk at the 1st Earth Microbiome Project in Shenzhen.

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  • 25K OTUs from cultured (70%), 10K from uncultured (30%). If the density of OTUs is the same between cultuted and uncluturedWe would expect around 140K OTUs from the uncultured15% 25K85%
  • There are 2934 A/B distinct species with genome projects /16458 total at NCBI
  • Nikos Kyrpides: The Microbial Earth Project

    1. 1. The Microbial Earth Project <br />Nikos Kyrpides<br />Genome Biology and MetagenomicsPrograms<br />DOE-Joint Genome Institute<br />The road to success in Metagenomics is through Microbial Genomics<br />
    2. 2. Binning<br />?<br />Metagenomic Analysis<br />Soil<br />Sargasso Sea<br />Termite Hindgut<br />Human Gut<br />Acid Mine Drainage<br />Reference Genomes<br />Species complexity<br />1 10 1001000 1000s 10000<br />The road to success in Metagenomics is through Microbial Genomics<br />Source: Susannah Tringe, JGI<br />
    3. 3. ?<br />Availability of Reference Genomes<br />Soil<br />Human gut<br />Termite Gut<br />Marine<br />Acid Mine Drainage<br />Reference Genomes<br />100%60% 50% 40% 20% 1%<br />
    4. 4. UNDERSTANDING vs INFORMATION<br />Do we really need more sequencing?<br />http://www.genomesonline.org<br />
    5. 5. Genome projects 2000<br />Genome projects 2010<br />11%<br />71 bacterial genomes<br />5500 bacterial genomes<br />Not much has changed the last 10 years<br />
    6. 6. Culturable<br />Unculturable<br />Minority Report<br />99% of microorganisms are not culturable with present methods.<br />
    7. 7. Rob Knight<br />~ 35,000 OTUs<br />Wu et al. Nature 2009<br />
    8. 8. Status of Archaeal & Bacterial (A/B) cultured species<br />
    9. 9. Wu et al. Nature 2009<br />
    10. 10. 2007-2011<br />GEBA<br />H-P Klenk<br />Goal:<br />Filling in the gaps in sequencing along the bacterial and archaeal branches of the <br />Tree of Life<br />Status:<br /><ul><li>>130 Complete
    11. 11. ~100 Draft
    12. 12. ~ 20 In progress</li></ul>Wu et al. Nature 2009<br />http://img.jgi.doe.gov/GEBA<br />
    13. 13. Genome coverage of cultured diversity<br />If we ll continue our current practices it will require over 60,000 genomes to cover the remaining 7,500 type strains <br />From 7,600 genome projects, only 13% of type strains <br />have been covered<br />Wu et al. Nature 2009<br />
    14. 14. Where do we go from here?<br />
    15. 15. GREAT CHALLENGES<br />P. Chain et al. Science, 2009<br />http://www.genomesonline.org<br />
    16. 16. DELUGE<br />OPPORTUNITY<br />AVALANCHE<br />FLOOD<br />TSUNAMI<br />
    17. 17. Microbial Earth Project<br />Acknowledgements<br />George Garrity<br />Phil Hugenholtz<br />H-P Klenk<br />
    18. 18. STEERING COMMITTEE<br />Nikos Kyrpides, DOE-JGI<br />George Garrity, Names4Life<br />Hans-Peter Klenk, DSMZ<br />Phil Hugenholtz, JGI<br />The Microbial Earth Project<br />Victor Kunin, JGI<br />Dino Liolios, GOLD<br />
    19. 19. Microbial Earth Project<br />
    20. 20. The Microbial Earth Project<br /> <br />Nikos C. Kyrpides1*, Philip Hugenholtz1,2, Markus Göker3, Victor Kunin1, Amrita Pati1, KonstantinosLiolios1, KonstantinosMavromatis1, Rudolf Amann4, Brian J. Beck5, Bruce W. Birren5a, Jim Bristow1, Patrick Chain1,6, Jongsik Chun7, Rita R. Colwell8, Antoine Danchin9, Edward F. DeLong10, John C. Detter1,6, Paul De Vos11, Peter Dawyndt11, Xiu-Zhu Dong12, Dusko S. Ehrlich13, Jonathan A. Eisen1,14, Claire Fraser15, Richard Gibbs16, Paul Glina17, Frank Oliver Glöckner18, Janet K. Jansson1,19, Jay, D. Keasling19,20, Jun Wang21, Rob Knight22, David Labeda23,Wen-Jun Li24, Victor Markowitz1,19, Edward R.B. Moore25, Mark Morrison26, Folker Meyer27, Karen E. Nelson28, Moriya Ohkuma29, Norman Pace30, Charles T. Parker31, Julian Parkhill32, Nan Qin21, Dorothea Rohlfs31, Ramon Rossello-Mora33, Eddy M. Rubin1, Johannes Sikorski3, David Smith34, Mitch Sogin35, Jung Sook Lee36, Rick Stevens27, Uli Stingl37, Ken Suzuki38, Jim M. Tiedje39, Brian Tindall3, Michael Wagner40, George Weinstock40a, Owen White15a, William B. Whitman41, Carl R. Woese41a, Lixin Zhang42, Genomic Standards Consortium, Dawn Field43, George M. Garrity31,39, and Hans-Peter Klenk3<br />
    21. 21. PARTNERS<br /><ul><li>GSC
    22. 22. CULTURE COLLECTION CENTERS
    23. 23. DSMZ [Hans-Peter Klenk]
    24. 24. ORGANISM SELECTION AND PRIORITIZATION
    25. 25. BERGEY’s, NAMES4LIFE[George Garrity, Barny Whitman]
    26. 26. REPRESENTATIVES FROM GRAND CHALLENGE PROJECTS
    27. 27. GEBA [Phil Hugenholtz, Jonathan Eisen]
    28. 28. TERRAGENOME [Janet Jansson, Jim Tiedje]
    29. 29. HMP [George Weinstock, Karen Nelson, Julian Parkhill]
    30. 30. CORE PARTICIPANTS
    31. 31. Large Sequencing Centers [JGI, BGI, JCVI, Sanger, Broad, WashU, Baylor]
    32. 32. Annotation/Analysis standards [Owen White, Folker Meyer, & GSC]</li></li></ul><li>
    33. 33. Strain / species diversity<br />
    34. 34. 10<br />Prochlorococcus marinus Pangenome<br />17<br />Listeria monocytogenes Pangenome<br />Staphylococcus aureus Pangenome<br />15<br />
    35. 35. PANGENOMES<br />HOW REPRESENTATIVE OF THE SPECIES IS THE PANGENOME?<br />PANGENOME<br />16S DIVERSITY<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />☺<br />
    36. 36. PANGENOMES<br />Enabling Technology for a new Microbiology<br />PANGENOME<br />POPULATION<br />SPECIFIC GENOTYPES<br />
    37. 37. PARADIGM SHIFTS<br />1960-1990<br />1990-2010<br />16S RNA<br />2010-2020<br />Genomes<br />Pangenomes<br />
    38. 38. What about Earth Microbiome?<br />
    39. 39.
    40. 40. Microbial Environmental Genomics Agency (MEGA)<br />

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