Welcome to the 1st International EMP meeting: The First 10,000 Pilot Study<br />Jack A Gilbert<br />
Argonne National Laboratory Institute for Genomic and Systems Biology<br />2<br />Once the diversity of the microbial worl...
Argonne National Laboratory Institute for Genomic and Systems Biology<br />www.earthmicrobiome.org<br />@gilbertjacka<br />
Exploring microbes from their perspective<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Gene...
The Earth Microbiome Project<br />>70 members, 30 institutes, 12 countries<br />Janet Jansson, Rob Knight, Jack A. Gilbert...
The Pilot Study EMP – The First 10,000 samples<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next...
 16S/18S rRNA survey and shotgun metagenomics</li></li></ul><li>Currently Public Metagenomes<br />US-EC Workshop on Marine...
Delmont et al., 2011. ISME J<br />
Earth Microbiome Project sites.<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Seq...
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
Alpha Diversity<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />5387 samples, <br />39,0...
What Does an EMP study look like?<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation S...
Continental-scale soil metagenomics project<br />Goals<br />Determine relative importance of edaphic and climatic drivers ...
Metagenomics shows the same pattern!<br /><ul><li>>800 subsystems identified
Mostly related to carbohydrates
At broadest level, highly conserved
Biomes clearly distinct
Vegetation is important
Little signal from climate or geography</li></ul>grasslands<br />forests<br />Poster board #1316<br />
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
Robust Seasonal Species Richness<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Se...
Argonne National Laboratory Institute for Genomic and Systems Biology<br />10,000 reads per sample<br />December 2007<br /...
Env. Parameter<br />Rhodobacteriales<br />Flavobacteriales<br />Rickettsiales<br />Pseudomonadales<br />Opitutales<br />Vi...
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
Environmental metabolome<br />
PRMT calculations for WCO data<br />PRMT1,2 = M x (E2 – E1)<br />Where PRMT1,2= vector of PRMT scores for all metabolites ...
http://www.bio.anl.gov/molecular_and_systems_biology/GilbertNetworks/Subnetworks/L4_DayNightTestAnim.gif<br />
Taxonomic Abundance<br />Linear Relationship between Taxonomic abundance and functional gene abundance<br />Microbial Asse...
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Jack Gilbert: Welcome to the 1st International EMP Meeting: the first 10,000 Pilot Study

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

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  • Total of 20 soil samples representing half the NEON sites with biological replicates.Also includes grassland soil samples from Fermilab experimental site.Shotgun metagenomic data generated with 454 as well as thorough characterization of soil samples – i.e. lots of metadata
  • Annotated shotgun metagenomic data using MG-RAST; binned sequences according to subsystems-approachPCA used to condense the data and inform regression analysis of metadata (next slide)
  • Jack Gilbert: Welcome to the 1st International EMP Meeting: the first 10,000 Pilot Study

    1. 1. Welcome to the 1st International EMP meeting: The First 10,000 Pilot Study<br />Jack A Gilbert<br />
    2. 2. Argonne National Laboratory Institute for Genomic and Systems Biology<br />2<br />Once the diversity of the microbial world is catalogued, <br />it will make astronomy look like a pitiful science.<br />- Julian Davies, Professor Emeritus, Microbiology and Immunology, UBC<br />
    3. 3. Argonne National Laboratory Institute for Genomic and Systems Biology<br />www.earthmicrobiome.org<br />@gilbertjacka<br />
    4. 4. Exploring microbes from their perspective<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />N-dimensional hypervolume and niche theory (mentioned by Tom Schmidt yesterday!)<br />Predict dynamics from environmental parameters<br />
    5. 5. The Earth Microbiome Project<br />>70 members, 30 institutes, 12 countries<br />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, <br />….. And you?<br />
    6. 6. The Pilot Study EMP – The First 10,000 samples<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br /><ul><li> 10,000 environmental samples
    7. 7. 16S/18S rRNA survey and shotgun metagenomics</li></li></ul><li>Currently Public Metagenomes<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />MG-RAST<br />>1500 users from 46 countries<br />>22,000 16S and shotgun metagenomes<br />>1 T base pairs of data.<br />Plagued by a lack of contextual data to characterize the environments<br />
    8. 8. Delmont et al., 2011. ISME J<br />
    9. 9. Earth Microbiome Project sites.<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />Currently >60,000 samples pledged from >50 Researchers<br />Sampled selected based on their position in environmental parameter gradients<br />Exceptionally rich contextualization collected at time of sequencing using MIxS checklist (Yilmaz et al., 2011 Nature Biotech) <br />
    10. 10. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
    11. 11. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
    12. 12. Alpha Diversity<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
    13. 13. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />5387 samples, <br />39,000 sequences per sample, <br />randomly resampled to 2000 reads per sample.<br />
    14. 14. What Does an EMP study look like?<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
    15. 15. Continental-scale soil metagenomics project<br />Goals<br />Determine relative importance of edaphic and climatic drivers on soil metagenomes <br />Pinpoint aspects of metagenomes that vary with those drivers.<br />Forests<br />Grasslands<br />Fermilab grasslands<br />Poster board #1316, Mon 10:45-12:30; Dion Antonopoulos, Sarah O’Brien, et al.<br />
    16. 16. Metagenomics shows the same pattern!<br /><ul><li>>800 subsystems identified
    17. 17. Mostly related to carbohydrates
    18. 18. At broadest level, highly conserved
    19. 19. Biomes clearly distinct
    20. 20. Vegetation is important
    21. 21. Little signal from climate or geography</li></ul>grasslands<br />forests<br />Poster board #1316<br />
    22. 22. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
    23. 23. Robust Seasonal Species Richness<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />Peaks on December 21st<br />Troughs on June 21st<br />
    24. 24. Argonne National Laboratory Institute for Genomic and Systems Biology<br />10,000 reads per sample<br />December 2007<br />2003<br /> 2004<br /> 2005<br /> 2006<br /> 2007<br /> 2008<br />20 million reads<br />>99.96% of all taxa were found in one month!<br />Caporasso et al. In preparation<br />
    25. 25. Env. Parameter<br />Rhodobacteriales<br />Flavobacteriales<br />Rickettsiales<br />Pseudomonadales<br />Opitutales<br />Vibrionales<br />Rhizobiales<br />Marine Microbial Assemblage Prediction (MMAP)<br />
    26. 26. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
    27. 27. Environmental metabolome<br />
    28. 28. PRMT calculations for WCO data<br />PRMT1,2 = M x (E2 – E1)<br />Where PRMT1,2= vector of PRMT scores for all metabolites in network<br />M = Connectivity Matrix for network<br />En= Vector of Normalized activity counts in metagenome n<br />Larsen et al, 2011, PLoS CB<br />TON TOC SRP<br />
    29. 29. http://www.bio.anl.gov/molecular_and_systems_biology/GilbertNetworks/Subnetworks/L4_DayNightTestAnim.gif<br />
    30. 30. Taxonomic Abundance<br />Linear Relationship between Taxonomic abundance and functional gene abundance<br />Microbial Assemblage Prediction (MAP)<br />Predictive Relative Metabolic Turnover (PRMT)<br />Environmental Parameters<br />Environmental Metabolome<br />
    31. 31.
    32. 32. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
    33. 33. Dominant microbes in the Western English Channel<br />Relative Concentration<br />Relative Abundance<br />Microbial Music<br />
    34. 34. US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />Rare Bloomers!<br />Microbes which demonstrate rapid increases in abundance for short periods.<br />
    35. 35. Requiem for a bacterial community!<br />US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing<br />
    36. 36. Acknowledgements<br />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.<br />Plymouth Marine Laboratory: Simon Thomas, Ben Temperton, Bonnie Laverock, Paul Somerfield, Ian Joint<br />CEH Oxford:Paul Swift and Dawn Field.<br />Josephine Bay Paul Centre: Mitch Sogin, Susan Huse<br />University of Colorado at Boulder: Rob Knight and Greg Caporaso<br />University of Southern California: Jed Furhman and Joshua Steele<br />University of Exeter: KonradPaszkiewicz<br />University of Lyon: Tim Vogel and Tom Dumont<br />Argonne National Laboratory Institute for Genomic and Systems Biology<br />
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