A phylogeny driven genomic encyclopedia of bacteria and archaea

(or what is GEBA anyway?)

Jonathan A. EisenOctober 27, 2009

From http://genomesonline.org

rRNA Tree of Life

The Tree is not Happy

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

Thermudesulfobacteria

Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

• At least 40 phyla of bacteria

As of 2002

Based on Hugenholtz, 2002

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

Thermudesulfobacteria

Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

• At least 40 phyla of bacteria

• Genome sequences are mostly from three phyla

As of 2002

Based on Hugenholtz, 2002

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

Thermudesulfobacteria

Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

• At least 40 phyla of bacteria

• Genome sequences are mostly from three phyla

• Some other phyla are only sparsely sampled

As of 2002

Based on Hugenholtz, 2002

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

Thermudesulfobacteria

Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

• At least 40 phyla of bacteria

• Genome sequences are mostly from three phyla

• Some other phyla are only sparsely sampled

• Same trend in Archaea

As of 2002

Based on Hugenholtz, 2002

Need for Tree Guidance Well Established

• Common approach within some eukaryotic groups

• Many small projects funded to fill in some bacterial or archaeal gaps

• Phylogenetic gaps in bacterial and archaeal projects commonly lamented in literature

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

Thermudesulfobacteria

Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

• At least 100 phyla of bacteria

• Genome sequences are mostly from three phyla

• Most phyla with cultured species are sparsely sampled

• Lineages with no cultured taxa even more poorly sampled

• Solution - use tree to really fill gaps

Well sampled phyla

http://www.jgi.doe.gov/programs/GEBA/pilot.html

GEBA Pilot Project Overview

• Identify major branches in rRNA tree for which no genomes are available

• Identify a cultured representative for each group

• Grow > 200 of these and prep. DNA• Sequence and finish 100• Annotate, analyze, release data• Assess benefits of tree guided sequencing

GEBA Pilot Project: Components• Project overview (Phil Hugenholtz, Nikos Kyrpides, Jonathan

Eisen, Eddy Rubin, Jim Bristow)• Project management (David Bruce, Eileen Dalin, Lynne Goodwin)• Culture collection and DNA prep (DSMZ, Hans-Peter Klenk)• Sequencing and closure (Eileen Dalin, Susan Lucas, Alla Lapidus,

Mat Nolan, Alex Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng)• Annotation and data release (Nikos Kyrpides, Victor Markowitz, et

al)• Analysis (Dongying Wu, Kostas Mavrommatis, Martin Wu, Victor

Kunin, Neil Rawlings, Ian Paulsen, Patrick Chain, Patrik D’Haeseleer, Sean Hooper, Iain Anderson, Amrita Pati, Natalia N. Ivanova, Athanasios Lykidis, Adam Zemla)

• Adopt a microbe education project (Cheryl Kerfeld)• Outreach (David Gilbert)• $$$ (DOE, Eddy Rubin, Jim Bristow)

Some Lessons From GEBA

GEBA Lesson 1

rRNA Tree of Life is a Useful Guide and Genomes Improve Resolution

GEBA Lesson 2

Phylogenetically Guided Selection Can Help Annotate Other Genomes

Most/All Functional Prediction Improves w/ Better Phylogenetic Sampling

• Better definition of protein family sequence “patterns”• Greatly improves “comparative” and “evolutionary”

based predictions• Conversion of hypothetical into conserved

hypotheticals• Linking distantly related members of protein families• Improved non-homology prediction

Kostas Mavrommatis

Natalia Ivanova

Thanos Lykidis

Nikos Kyrpides

Iain Anderson

GEBA Lesson 3

Phylogenetically Guided Selection Can Help Study Uncultured

Organisms

Environmental Shotgun Sequencing

shotgun

sequence

ABCDEFG

TUVWXYZ

Binning challenge

Metagenomic Analysis Improves

Sean Hooper

Amrita Pati

• Small but real improvement in metagenomic annotation and analysis

GEBA Lesson 4

We have still only scratched the surface of microbial diversity

Protein Family Rarefaction Curves

• Take data set of multiple complete genomes• Identify all protein families using MCL• Plot # of genomes vs. # of protein families

Phylogenetic Distribution Novelty: 1st Bacterial Actin Related Protein

Haliangium ochraceum DSM 14365

Victor Kunin

Patrik D’haeseleer

Adam Zemla

Phylogenetic Diversity with GEBA

Phylogenetic Diversity: Isolates

Phylogenetic Diversity: All

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi

FirmicutesFusobacteria Actinobacteria

Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira

SynergistesDeferribacteres

Thermudesulfobacteria

Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

• At least 40 phyla of bacteria

• Genome sequences are mostly from three phyla

• Most phyla with cultured species are sparsely sampled

• Lineages with no cultured taxa even more poorly sampled

Well sampled phylaPoorly sampled

No cultured taxa

Uncultured Lineages:Technical Approaches

• Get into culture• Enrichment cultures• If abundant in low diversity ecosystems• Flow sorting• Microbeads• Microfluidic sorting• Single cell amplification

GEBA Lesson 6

Need Experiments from Across the Tree of Life too

Adopt a Microbe

MICROBES

A Happy Tree of Life

Related Lesson 1

METADATA ROCKS

SIGS

• The Genomic Standards Consortium • The GSC is an open-membership working body which

formed in September 2005. • The goal of this international community is to promote

mechanisms that standardize the description of genomes and the exchange and integration of genomic data.

• See http://gensc.org/gc_wiki/index.php/Main_Page