Jack Gilbert's talk at the 1st Earth Microbiome Meeting in Shenzhen

1. Welcome to the 1st International EMP meeting: The First 10,000 Pilot Study Jack A Gilbert

2. Argonne National Laboratory Institute for Genomic and Systems Biology 2 Once the diversity of the microbial world is catalogued, it will make astronomy look like a pitiful science. - Julian Davies, Professor Emeritus, Microbiology and Immunology, UBC

3. Argonne National Laboratory Institute for Genomic and Systems Biology www.earthmicrobiome.org @gilbertjacka

4. Exploring microbes from their perspective US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing N-dimensional hypervolume and niche theory (mentioned by Tom Schmidt yesterday!) Predict dynamics from environmental parameters

5. The Earth Microbiome Project >70 members, 30 institutes, 12 countries Janet Jansson, Rob Knight, Jack A. Gilbert, Bin Hu, Noah Fierer, Folker Meyer, Rick Stevens, Jonathan A Eisen, Jed Furhman, Mark Bailey, Jeff Gordon, Norman Pace, JeroenRaes, James Tiedje, Ruth Ley, Noah Fierer, Dawn Field, Nikos Kyrpides, Frank-Oliver Glockner, Hans-Peter Klenk, K. Eric Wommack, Elizabeth M. Glass, Kathryn Docherty, Rachel Gallery,, George Kowalchuk, Mark Bailey, Dion Antonopoulos, PavanBalaji, C. Titus Brown, Christopher T. Brown, NarayanDesai, Dirk Evers, Wu Feng, Daniel Huson, James Knight, Eugene Kolker, Kostas Konstantindis, Joel Kostka, Rachel Mackelprang, Alice McHardy, Christopher Quince, Alexander Sczyrba, Ashley Shade, ….. And you?

8. Delmont et al., 2011. ISME J

9. Earth Microbiome Project sites. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing Currently >60,000 samples pledged from >50 Researchers Sampled selected based on their position in environmental parameter gradients Exceptionally rich contextualization collected at time of sequencing using MIxS checklist (Yilmaz et al., 2011 Nature Biotech)

10. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing

11. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing

12. Alpha Diversity US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing

13. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing 5387 samples, 39,000 sequences per sample, randomly resampled to 2000 reads per sample.

14. What Does an EMP study look like? US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing

15. Continental-scale soil metagenomics project Goals Determine relative importance of edaphic and climatic drivers on soil metagenomes Pinpoint aspects of metagenomes that vary with those drivers. Forests Grasslands Fermilab grasslands Poster board #1316, Mon 10:45-12:30; Dion Antonopoulos, Sarah O’Brien, et al.

17. Mostly related to carbohydrates

18. At broadest level, highly conserved

19. Biomes clearly distinct

20. Vegetation is important

21. Little signal from climate or geographygrasslands forests Poster board #1316

22. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing

23. Robust Seasonal Species Richness US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing Peaks on December 21st Troughs on June 21st

24. Argonne National Laboratory Institute for Genomic and Systems Biology 10,000 reads per sample December 2007 2003 2004 2005 2006 2007 2008 20 million reads >99.96% of all taxa were found in one month! Caporasso et al. In preparation

25. Env. Parameter Rhodobacteriales Flavobacteriales Rickettsiales Pseudomonadales Opitutales Vibrionales Rhizobiales Marine Microbial Assemblage Prediction (MMAP)

26. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing

27. Environmental metabolome

28. PRMT calculations for WCO data PRMT1,2 = M x (E2 – E1) Where PRMT1,2= vector of PRMT scores for all metabolites in network M = Connectivity Matrix for network En= Vector of Normalized activity counts in metagenome n Larsen et al, 2011, PLoS CB TON TOC SRP

29. http://www.bio.anl.gov/molecular_and_systems_biology/GilbertNetworks/Subnetworks/L4_DayNightTestAnim.gif

30. Taxonomic Abundance Linear Relationship between Taxonomic abundance and functional gene abundance Microbial Assemblage Prediction (MAP) Predictive Relative Metabolic Turnover (PRMT) Environmental Parameters Environmental Metabolome

32. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing

33. Dominant microbes in the Western English Channel Relative Concentration Relative Abundance Microbial Music

34. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing Rare Bloomers! Microbes which demonstrate rapid increases in abundance for short periods.

35. Requiem for a bacterial community! US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing

36. Acknowledgements Argonne National Laboratory & University of Chicago: Folker Meyer, Kevin Keegan, Jared Wilkening, Andreas Wilkes, Sarah Owens, Ella Rakowski, Peter Larsen, Dion Antonopolous, Sarah O’Brien, Kevin Keegen, et al. Plymouth Marine Laboratory: Simon Thomas, Ben Temperton, Bonnie Laverock, Paul Somerfield, Ian Joint CEH Oxford:Paul Swift and Dawn Field. Josephine Bay Paul Centre: Mitch Sogin, Susan Huse University of Colorado at Boulder: Rob Knight and Greg Caporaso University of Southern California: Jed Furhman and Joshua Steele University of Exeter: KonradPaszkiewicz University of Lyon: Tim Vogel and Tom Dumont Argonne National Laboratory Institute for Genomic and Systems Biology