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)