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

1. The Microbial Earth Project Nikos Kyrpides Genome Biology and MetagenomicsPrograms DOE-Joint Genome Institute The road to success in Metagenomics is through Microbial Genomics

2. Binning ? Metagenomic Analysis Soil Sargasso Sea Termite Hindgut Human Gut Acid Mine Drainage Reference Genomes Species complexity 1 10 1001000 1000s 10000 The road to success in Metagenomics is through Microbial Genomics Source: Susannah Tringe, JGI

3. ? Availability of Reference Genomes Soil Human gut Termite Gut Marine Acid Mine Drainage Reference Genomes 100%60% 50% 40% 20% 1%

4. UNDERSTANDING vs INFORMATION Do we really need more sequencing? http://www.genomesonline.org

5. Genome projects 2000 Genome projects 2010 11% 71 bacterial genomes 5500 bacterial genomes Not much has changed the last 10 years

6. Culturable Unculturable Minority Report 99% of microorganisms are not culturable with present methods.

7. Rob Knight ~ 35,000 OTUs Wu et al. Nature 2009

8. Status of Archaeal & Bacterial (A/B) cultured species

9. Wu et al. Nature 2009

11. ~100 Draft

12. ~ 20 In progressWu et al. Nature 2009 http://img.jgi.doe.gov/GEBA

13. Genome coverage of cultured diversity If we ll continue our current practices it will require over 60,000 genomes to cover the remaining 7,500 type strains From 7,600 genome projects, only 13% of type strains have been covered Wu et al. Nature 2009

14. Where do we go from here?

15. GREAT CHALLENGES P. Chain et al. Science, 2009 http://www.genomesonline.org

16. DELUGE OPPORTUNITY AVALANCHE FLOOD TSUNAMI

17. Microbial Earth Project Acknowledgements George Garrity Phil Hugenholtz H-P Klenk

18. STEERING COMMITTEE Nikos Kyrpides, DOE-JGI George Garrity, Names4Life Hans-Peter Klenk, DSMZ Phil Hugenholtz, JGI The Microbial Earth Project Victor Kunin, JGI Dino Liolios, GOLD

19. Microbial Earth Project

20. The Microbial Earth Project 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

22. CULTURE COLLECTION CENTERS

23. DSMZ [Hans-Peter Klenk]

24. ORGANISM SELECTION AND PRIORITIZATION

25. BERGEY’s, NAMES4LIFE[George Garrity, Barny Whitman]

26. REPRESENTATIVES FROM GRAND CHALLENGE PROJECTS

27. GEBA [Phil Hugenholtz, Jonathan Eisen]

28. TERRAGENOME [Janet Jansson, Jim Tiedje]

29. HMP [George Weinstock, Karen Nelson, Julian Parkhill]

30. CORE PARTICIPANTS

31. Large Sequencing Centers [JGI, BGI, JCVI, Sanger, Broad, WashU, Baylor]

33. Strain / species diversity

34. 10 Prochlorococcus marinus Pangenome 17 Listeria monocytogenes Pangenome Staphylococcus aureus Pangenome 15

35. PANGENOMES HOW REPRESENTATIVE OF THE SPECIES IS THE PANGENOME? PANGENOME 16S DIVERSITY ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺ ☺

36. PANGENOMES Enabling Technology for a new Microbiology PANGENOME POPULATION SPECIFIC GENOTYPES

37. PARADIGM SHIFTS 1960-1990 1990-2010 16S RNA 2010-2020 Genomes Pangenomes

38. What about Earth Microbiome?

40. Microbial Environmental Genomics Agency (MEGA)