jack gilbert: welcome to the 1st international emp meeting: the first 10,000 pilot study
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Welcome to the 1st International EMP meeting: The First 10,000 Pilot Study
Jack A Gilbert
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
Argonne National Laboratory Institute for Genomic and Systems Biology
www.earthmicrobiome.org
@gilbertjacka
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
Exploring microbes from their perspective
N-dimensional hypervolume and niche theory (mentioned by Tom Schmidt yesterday!)
Predict dynamics from environmental parameters
The Earth Microbiome Project
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, Jeroen Raes, 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, Pavan Balaji, C. Titus Brown, Christopher T. Brown, Narayan Desai, 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?
>70 members, 30 institutes, 12 countries
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
The Pilot Study EMP – The First 10,000 samples
• 10,000 environmental samples• 16S/18S rRNA survey and shotgun metagenomics
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
Currently Public Metagenomes
Plagued by a lack of contextual data to characterize the environments
MG-RAST
>1500 users from 46 countries
>22,000 16S and shotgun metagenomes
>1 T base pairs of data.
A
B
0
10
20
30
40
50
60
70
80
90
0 200 400 600 800 1000 1200 1400Sequence length generated (bp)
OceansCoral atollsDeep oceansAntarctic lakesArctic snow
SoilsSedimentsSludgesMFCAcid mine
Polluted airHuman fecesChicken ceacumMouse ceacumCow rumen
Perc
enta
geof
ann
otat
edse
quen
ces
1 =15.16%
λ2=8.10%
λ
A
0204060
80100120
Delmont et al., ISMEj (2011)
Delmont et al., 2011. ISME J
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
Earth Microbiome Project sites.
Exceptionally rich contextualization collected at time of sequencing using MIxS checklist (Yilmaz et al., 2011 Nature Biotech)
Currently >60,000 samples pledged from >50 Researchers
Sampled selected based on their position in environmental parameter gradients
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
Alpha Diversity
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.
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
What Does an EMP study look like?
Goals
Determine relative importance of edaphic and climatic drivers on soil metagenomes
Pinpoint aspects of metagenomes that vary with those drivers.
Forests
Fermilab grasslands
Grasslands
Poster board #1316, Mon 10:45-12:30; Dion Antonopoulos, Sarah O’Brien, et al.
Continental-scale soil metagenomics project
Metagenomics shows the same pattern!
grasslands
forests
Poster board #1316
• >800 subsystems identified• Mostly related to
carbohydrates• At broadest level, highly
conserved
• Biomes clearly distinct • Vegetation is important• Little signal from climate or
geography
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
Robust Seasonal Species Richness
4.5
5
5.5
6
6.5
0 200 400 600 800 1000 1200 1400 1600 1800 2000 2200
D
Log (S)
Peaks on December 21st
Troughs on June 21st
Argonne National Laboratory Institute for Genomic and Systems Biology
December 2007
10,000 reads per sample
20 million reads
2003 2004 2005 2006 2007 2008
>99.96% of all taxa were found in one
month!
Caporasso et al. In preparation
Marine Microbial Assemblage Prediction (MMAP)
parent
jijijji cvTT ,,
Env. Parameter
Rhodobacteriales
Flavobacteriales
Rickettsiales
Pseudomonadales
Opitutales
Vibrionales
Rhizobiales
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
Environmental metabolome
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 CBTON TOC SRP
http://www.bio.anl.gov/molecular_and_systems_biology/GilbertNetworks/Subnetworks/L4_DayNightTestAnim.gif
Environmental Parameters
Linear Relationship
between Taxonomic
abundance and functional gene
abundance
Predictive Relative
Metabolic Turnover (PRMT)
Microbial Assemblage Prediction
(MAP)
Taxonomic Abundance
Environmental Metabolome
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
Rela
tive
Abun
danc
eRe
lativ
e Co
ncen
trati
on
Microbial Music
Dominant microbes in the Western English Channel
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.
US-EC Workshop on Marine Genomics: Next Generation Scientists for Next Generation Sequencing
Requiem for a bacterial community!
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: Konrad Paszkiewicz University of Lyon: Tim Vogel and Tom Dumont
Argonne National Laboratory Institute for Genomic and Systems Biology
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