nikos kyrpides: the microbial earth project
DESCRIPTION
Nikos Kyrpides talk at the 1st Earth Microbiome Project in Shenzhen.TRANSCRIPT
The Microbial Earth Project
Nikos Kyrpides
Genome Biology and Metagenomics Programs
DOE-Joint Genome Institute
The road to success in Metagenomics is through Microbial Genomics
Binning
Acid Mine Drainage Sargasso Sea Soil
1 10 100 1000 1000s 10000
Species complexity
Human GutTermite Hindgut
?The road to success in Metagenomics is through Microbial Genomics
Source: Susannah Tringe, JGI
Reference Genomes
Acid Mine Drainage Human gut Soil
100% 60% 50% 40% 20% 1%
Reference Genomes
Termite GutMarine
?
JGI17%
J VENTER13%
BROAD11%
WashU6%
BCM4%
IGS4%
WORLD45%
Sequencing Centers for Archaea & BacteriaJUNE 2011: 7,739 projects
35%
12%7%
46%
Complete Genomes: 1619
JGI
J VENTER
Sanger
WORLD
http://www.genomesonline.org
Proteobacteria
45%
Actinobacteria
7%
Low G+C gram
positives
24%
other divisions
24%
71 bacterial genomes
Genome projects 2000
Proteobacteria
39%
Actinobacteria
18%
Firmicutes
28%
other phyla
18%
5500 bacterial genomes
Genome projects 2010
11%
Culturable
Unculturable
• 99% of microorganisms
are not culturable with
present methods.
Wu et al. Nature 2009
15%
85%
16S distance
cultured uncultured
Rob
Knight
~ 35,000 OTUs
cultured A/B in culture collections
> 600,000
with 16S
~ 30,000
type strains
~ 9,000
A/B strains with genome projects
~ 7,600
type strains
1,450
with sequence data
865
Wu et al. Nature 2009
GEBA
Goal:
Filling in the gaps in
sequencing along the
bacterial and archaeal
branches of the
Tree of Life
Wu et al. Nature 2009
Status:
• >130 Complete
• ~100 Draft
• ~ 20 In progress
http://img.jgi.doe.gov/GEBA
2007-2011
H-P Klenk
Wu et al. Nature 2009
From 7,600 genome projects, only 13% of type strains
have been covered
If we ll continue our current practices it will require
over 60,000 genomes to cover the remaining 7,500
type strains
1995-2009 2010-2015
Finished 1000 3000
Draft 1000 10000
Genes 8 Million 52 Million
P. Chain et al. Science, 2009
2010-2013
3,000
20,000
92 Million
http://www.genomesonline.org
George GarrityH-P Klenk Phil Hugenholtz
Victor Kunin, JGI
Dino Liolios, GOLD
STEERING COMMITTEE
Nikos Kyrpides, DOE-JGI
George Garrity, Names4Life
Hans-Peter Klenk, DSMZ
Phil Hugenholtz, JGI
The Microbial Earth Project
• Nikos C. Kyrpides1*, Philip Hugenholtz1,2, Markus Göker3, Victor Kunin1, Amrita
Pati1, Konstantinos Liolios1, Konstantinos Mavromatis1, 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
62 Authors
13 Countries
GSC
CULTURE COLLECTION CENTERS
DSMZ [Hans-Peter Klenk]
ORGANISM SELECTION AND PRIORITIZATION
BERGEY’s, NAMES4LIFE [George Garrity, Barny Whitman]
REPRESENTATIVES FROM GRAND CHALLENGE PROJECTS
GEBA [Phil Hugenholtz, Jonathan Eisen]
TERRAGENOME [Janet Jansson, Jim Tiedje]
HMP [George Weinstock, Karen Nelson, Julian Parkhill]
CORE PARTICIPANTS
Large Sequencing Centers [JGI, BGI, JCVI, Sanger, Broad, WashU, Baylor]
Annotation/Analysis standards [Owen White, Folker Meyer, & GSC]
Prochlorococcus marinus Pangenome10
Listeria monocytogenes Pangenome
17
15
Staphylococcus aureus Pangenome
1. How representative is the pangenome phylogenetically?
PANGENOME
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16S DIVERSITY
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2. How representative is it geographically?
Comparison of pangenomes with natural populations
PANGENOME POPULATION
SPECIFIC GENOTYPES
EnvoTypes
Geographic Isolation
Habitat
Community makeup
What are the factors contributing to specific “genotypes”?
1960-1990
16S RNA
1990-2010
Genomes
2010-2020
Pangenomes
Microbial Environmental Genomics Agency (MEGA)