Jack Gilbert: Welcome to the 1st International EMP Meeting: the first 10,000 Pilot Study

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


www.earthmicrobiome.org

@gilbertjacka

http://www.earthmicrobiome.org/

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


The Pilot Study EMP – The First 10,000 samples

• 10,000 environmental samples• 16S/18S rRNA survey and shotgun metagenomics


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


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


Alpha Diversity


5387 samples, 39,000 sequences per sample, randomly resampled to 2000 reads per sample.


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


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


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

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

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

Rela

tive

Abun

danc

eRe

lativ

e Co

ncen

trati

on

Microbial Music

Dominant microbes in the Western English Channel


Rare Bloomers!

Microbes which demonstrate rapid increases in abundance for short periods.


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


Jack Gilbert: Welcome to the 1st International EMP Meeting: the first 10,000 Pilot Study

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