Jonathan Eisen talk at ASM General Meeting 2010

A phylogeny driven genomic encyclopedia of bacteria and archaea

Jonathan A. Eisen

Talk at ASMGMMay 25, 2010

Tuesday, May 25, 2010

Fleischmann et al. 1995


Microbial genomes

From http://genomesonline.orgTuesday, May 25, 2010

rRNA Tree of Life

FIgure from Barton, Eisen et al. “Evolution”, CSHL Press.

Based on tree from Pace NR, 2003.

Archaea

Eukaryotes

Bacteria


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

2002

Based on Hugenholtz, 2002


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter


• Genome sequences are mostly from three phyla


2002


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter



• Some other phyla are only sparsely sampled


2002


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Same trend in ArchaeaBased on Hugenholtz, 2002

2002


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Same trend in EukaryotesBased on Hugenholtz, 2002

2002


The Tree is not Happy



Archaea

Eukaryotes

Bacteria


Why Increase Phylogenetic Coverage?

• Common approach within some eukaryotic groups

• Many small projects to fill in bacterial or archaeal gaps

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

• Many potential benefits


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Solution I: sequence more phyla

• NSF-funded Tree of Life Project

• A genome from each of eight phyla

Eisen & Ward, PIs


The Tree of Life is Still Angry



Eukaryotes

Bacteria

Archaea


Major Lineages of Actinobacteria2.5.1 Acidimicrobidae2.5.1.1 Unclassified2.5.1.2 "Microthrixineae2.5.1.3 Acidimicrobineae2.5.1.4 BD2-102.5.1.5 EB10172.5.2 Actinobacteridae2.5.2.1 Unclassified2.5.2.10 Ellin306/WR1602.5.2.11 Ellin50122.5.2.12 Ellin50342.5.2.13 Frankineae2.5.2.14 Glycomyces2.5.2.15 Intrasporangiaceae2.5.2.16 Kineosporiaceae2.5.2.17 Microbacteriaceae2.5.2.18 Micrococcaceae2.5.2.19 Micromonosporaceae2.5.2.2 Actinomyces2.5.2.20 Propionibacterineae2.5.2.21 Pseudonocardiaceae2.5.2.22 Streptomycineae2.5.2.23 Streptosporangineae2.5.2.3 Actinomycineae2.5.2.4 Actinosynnemataceae2.5.2.5 Bifidobacteriaceae2.5.2.6 Brevibacteriaceae2.5.2.7 Cellulomonadaceae2.5.2.8 Corynebacterineae2.5.2.9 Dermabacteraceae2.5.3 Coriobacteridae2.5.3.1 Unclassified2.5.3.2 Atopobiales2.5.3.3 Coriobacteriales2.5.3.4 Eggerthellales2.5.4 OPB412.5.5 PK12.5.6 Rubrobacteridae2.5.6.1 Unclassified2.5.6.2 "Thermoleiphilaceae2.5.6.3 MC472.5.6.4 Rubrobacteraceae

2.5 Actinobacteria2.5.1 Acidimicrobidae2.5.1.1 Unclassified2.5.1.2 "Microthrixineae2.5.1.3 Acidimicrobineae2.5.1.3.1 Unclassified2.5.1.3.2 Acidimicrobiaceae2.5.1.4 BD2-102.5.1.5 EB10172.5.2 Actinobacteridae2.5.2.1 Unclassified2.5.2.10 Ellin306/WR1602.5.2.11 Ellin50122.5.2.12 Ellin50342.5.2.13 Frankineae2.5.2.13.1 Unclassified2.5.2.13.2 Acidothermaceae2.5.2.13.3 Ellin60902.5.2.13.4 Frankiaceae2.5.2.13.5 Geodermatophilaceae2.5.2.13.6 Microsphaeraceae2.5.2.13.7 Sporichthyaceae2.5.2.14 Glycomyces2.5.2.15 Intrasporangiaceae2.5.2.15.1 Unclassified2.5.2.15.2 Dermacoccus2.5.2.15.3 Intrasporangiaceae2.5.2.16 Kineosporiaceae2.5.2.17 Microbacteriaceae2.5.2.17.1 Unclassified2.5.2.17.2 Agrococcus2.5.2.17.3 Agromyces2.5.2.18 Micrococcaceae2.5.2.19 Micromonosporaceae2.5.2.2 Actinomyces2.5.2.20 Propionibacterineae2.5.2.20.1 Unclassified2.5.2.20.2 Kribbella2.5.2.20.3 Nocardioidaceae2.5.2.20.4 Propionibacteriaceae2.5.2.21 Pseudonocardiaceae2.5.2.22 Streptomycineae2.5.2.22.1 Unclassified2.5.2.22.2 Kitasatospora2.5.2.22.3 Streptacidiphilus2.5.2.23 Streptosporangineae2.5.2.23.1 Unclassified2.5.2.23.2 Ellin51292.5.2.23.3 Nocardiopsaceae2.5.2.23.4 Streptosporangiaceae2.5.2.23.5 Thermomonosporaceae2.5.2.3 Actinomycineae2.5.2.4 Actinosynnemataceae2.5.2.5 Bifidobacteriaceae2.5.2.6 Brevibacteriaceae2.5.2.7 Cellulomonadaceae2.5.2.8 Corynebacterineae2.5.2.8.1 Unclassified2.5.2.8.2 Corynebacteriaceae2.5.2.8.3 Dietziaceae2.5.2.8.4 Gordoniaceae2.5.2.8.5 Mycobacteriaceae2.5.2.8.6 Rhodococcus2.5.2.8.7 Rhodococcus2.5.2.8.8 Rhodococcus2.5.2.9 Dermabacteraceae2.5.2.9.1 Unclassified2.5.2.9.2 Brachybacterium2.5.2.9.3 Dermabacter2.5.3 Coriobacteridae2.5.3.1 Unclassified2.5.3.2 Atopobiales2.5.3.3 Coriobacteriales2.5.3.4 Eggerthellales2.5.4 OPB412.5.5 PK12.5.6 Rubrobacteridae2.5.6.1 Unclassified2.5.6.2 "Thermoleiphilaceae2.5.6.2.1 Unclassified2.5.6.2.2 Conexibacter2.5.6.2.3 XGE5142.5.6.3 MC472.5.6.4 Rubrobacteraceae


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter



• 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.htmlTuesday, May 25, 2010

A Genomic Encyclopedia of Bacteria and Archaea (GEBA)


GEBA Pilot Project Overview

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

• Identify branches with a cultured representative in DSMZ

• Grow > 200 of these and prep. DNA• Sequence and finish 100 (covering breadth

of bacterial/archaea diversity)• Annotate, analyze, release data• Assess benefits of tree guided sequencing


GEBA and Openness

• All data released as quickly as possible w/ no restrictions to IMG-GEBA; Genbank, etc

• Data also available in Biotorrents (http://biotorrents.net)

• Individual genome reports published in OA “Standards in Genome Sciences (SIGS)”

• 1st GEBA paper in Nature freely available and published using Creative Commons License


http://biotorrents.net

http://biotorrents.net

GEBA Lesson 1

rRNA Tree is Useful for Identifying Phylogenetically Novel Genomes


rRNA Tree of Life



Archaea

Eukaryotes

Bacteria


Network of Life

Figure from Barton, Eisen et al. “Evolution”, CSHL Press.


Archaea

Eukaryotes

Bacteria


Whole Genome Tree w/ AMPHORA

http://bobcat.genomecenter.ucdavis.edu/AMPHORA/See Wu and Eisen, Genome Biology 2008 9: R151


http://bobcat.genomecenter.ucdavis.edu/AMPHORA/




Compare PD in Trees


PD of rRNA, Genome Trees Similar

From Wu et al. 2009 Nature 462, 1056-1060Tuesday, May 25, 2010

http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html


GEBA Lesson 1B

rRNA Tree topology is not perfect;Genome-based trees better


16s Says Hyphomonas is in Rhodobacteriales

Badger et al. 2005

28Tuesday, May 25, 2010

WGT and individual gene trees:Its Related to Caulobacterales

Badger et al. 2005

29Tuesday, May 25, 2010

Wh

Concatenated alignment “whole genome tree” built using AMPHORA


Whole genome phylogeny?• Many approaches

– Gene presence/absence– Concatenation of phylogenetic markers– Separate phylogeny of genes and then

integration of results (e.g., networks)– Models that incorporate gain/loss as well as

gene phylogeny• No new results from us

– However ... see Eric Alm talk Ballroom A - “Microbes in a changing world” session tomorrow AM


GEBA Lesson 2

Phylogeny-driven genome selection helps discover new genetic diversity


Network of Life



Archaea

Eukaryotes

Bacteria


Protein Family Rarefaction Curves

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


Synapomorphies exist


GEBA Lesson 3

Phylogeny-driven genome selection improves genome annotation


Predicting Function

• Key step in genome projects• More accurate predictions help guide

experimental and computational analyses• Many diverse approaches• Comparative and evolutionary analysis

greatly improves most predictions


Most/All Functional Prediction Improves w/ Better Phylogenetic Sampling

• Better definition of protein family sequence “patterns” (e.g., improved HMMs)

• Conversion of hypothetical into conserved hypotheticals

• Greatly improves “comparative” and “evolutionary” based predictions

• Linking distantly related members of protein families

• Improved non-homology prediction


From Wu et al. 2009.Tuesday, May 25, 2010



GEBA Lesson 4

Phylogeny-driven genome selection improves analysis of genome data

from uncultured organisms


Metagenomics Challenge


Metagenomics Challenge

1. Who is out there? 2. What are they doing?


Who is out there?

• Mimic rRNA PCR based studies• But can now do these with other genes


rRNA phylotyping from metagenomics

Venter et al., 2004


Shotgun Sequencing Allows Use of Alternative Anchors (e.g., RecA)

Venter et al., 2004


0

0.1250

0.2500

0.3750

0.5000

Alphaproteobacteria

Betaproteobacteria

Gammaproteobacteria

Epsilonproteobacteria

Deltaproteobacteria

Cyanobacteria

Firmicutes

Actinobacteria

Chlorobi

CFB

Chloroflexi

Spirochaetes

Fusobacteria

Deinococcus-Thermus

Euryarchaeota

Crenarchaeota

Sargasso Phylotypes

Wei

ght

ed %

of

Clo

nes

Major Phylogenetic Group

EFGEFTuHSP70RecARpoBrRNA

Shotgun Sequencing Allows Use of Other Markers

Venter et al., 2004


0

0.1250

0.2500

0.3750

0.5000

Alphaproteobacteria

Betaproteobacteria

Gammaproteobacteria

Epsilonproteobacteria

Deltaproteobacteria

Cyanobacteria

Firmicutes

Actinobacteria

Chlorobi

CFB

Chloroflexi

Spirochaetes

Fusobacteria

Deinococcus-Thermus

Euryarchaeota

Crenarchaeota

Sargasso Phylotypes

Wei

ght

ed %

of

Clo

nes

Major Phylogenetic Group

EFGEFTuHSP70RecARpoBrRNA

Shotgun Sequencing Allows Use of Other Markers

Venter et al., 2004

Should improve with better genomic sampling


Functional Inference from Metagenomics

• Can work well for individual genes• Predicting “community” function is

challenging because treating community as a bag of genes does not work well

• Better to “compartmentalize” data ...


ABCDEFG

TUVWXYZ

Binning challenge


ABCDEFG

TUVWXYZ

Binning challenge

Best binning method: reference genomes


Reference Genomes Coming from Select Environment


ABCDEFG

TUVWXYZ

Binning challenge

No reference genome? What do you do?


ABCDEFG

TUVWXYZ

Binning challenge

No reference genome? What do you do?

Phylogeny ....Tuesday, May 25, 2010

AMPHORA

Guide treeTuesday, May 25, 2010

Phylogenetic Binning Using AMPHORA

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

Alph

apro

teob

acteria

Betapr

oteo

bacter

ia

Gammap

roteob

acteria

Deltapr

oteo

bacter

ia

Epsil

onpr

oteo

bacter

ia

Uncla

ssified

Pro

teob

acteria

Cyan

obac

teria

Chlamyd

iae

Acidob

acteria

Bacter

oide

tes

Actin

obac

teria

Aquific

ae

Plan

ctom

ycetes

Spiro

chae

tes

Firmicu

tes

Chloro

flexi

Chloro

bi

Uncla

ssified

Bac

teria

dnaGfrrinfCnusApgkpyrGrplArplBrplCrplDrplErplFrplKrplLrplMrplNrplPrplSrplTrpmArpoBrpsBrpsCrpsErpsIrpsJrpsKrpsMrpsSsmpBtsf

AMPHORA - each read on its own treeTuesday, May 25, 2010


0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

Alph

apro

teob

acteria

Betapr

oteo

bacter

ia

Gammap

roteob

acteria

Deltapr

oteo

bacter

ia

Epsil

onpr

oteo

bacter

ia

Uncla

ssified

Pro

teob

acteria

Cyan

obac

teria

Chlamyd

iae

Acidob

acteria

Bacter

oide

tes

Actin

obac

teria

Aquific

ae

Plan

ctom

ycetes

Spiro

chae

tes

Firmicu

tes

Chloro

flexi

Chloro

bi

Uncla

ssified

Bac

teria


AMPHORA - each read on its own tree

Should improve with better genomic sampling


Metagenomic Analysis Improves w/ Phylogenetic Sampling

• Small but real improvements in– Gene identification / confirmation– Functional prediction– Binning– Phylogenetic classification


Metagenomic Analysis Improves w/ Phylogenetic Sampling

• Small but real improvements in– Gene identification / confirmation– Functional prediction– Binning– Phylogenetic classification

• But not a lot ...


How to improve phylogenetic analysis of metagenomic data

• Fragmented data

• Which genes to use?

• More automation


iSEEM Project


Phylogenetic challenge

A single tree with everything



0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

Alph

apro

teob

acteria

Betapr

oteo

bacter

ia

Gammap

roteob

acteria

Deltapr

oteo

bacter

ia

Epsil

onpr

oteo

bacter

ia

Uncla

ssified

Pro

teob

acteria

Cyan

obac

teria

Chlamyd

iae

Acidob

acteria

Bacter

oide

tes

Actin

obac

teria

Aquific

ae

Plan

ctom

ycetes

Spiro

chae

tes

Firmicu

tes

Chloro

flexi

Chloro

bi

Uncla

ssified

Bac

teria



Improves with better phylogenetic methods



0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

Alph

apro

teob

acteria

Betapr

oteo

bacter

ia

Gammap

roteob

acteria

Deltapr

oteo

bacter

ia

Epsil

onpr

oteo

bacter

ia

Uncla

ssified

Pro

teob

acteria

Cyan

obac

teria

Chlamyd

iae

Acidob

acteria

Bacter

oide

tes

Actin

obac

teria

Aquific

ae

Plan

ctom

ycetes

Spiro

chae

tes

Firmicu

tes

Chloro

flexi

Chloro

bi

Uncla

ssified

Bac

teria



Improves with more gene families


New “Marker Genes”

• 100 representative genomes• MCL gene families• Identify gene families w/

– High universality– High uniformity of copy number– Phylogenetic tree similar to “whole genome

tree”


0 1 2 3 4 5 6

rRNA16SruvBnusArplBpurArpsJsecYrpsIpyrHrpsErplPrplNrpsCruvArplFrplAserSrplKrpsKpriAsmpBrpsGguaArpsQrpsLrplUrplOrpsMinfCrplSrplVrplCrpsPrplErplTrplLrplQrpsHmraWrpsOrpsBrplIrplMrplRttffrrtsfrplDradArpsStrmDcoaErpmA

0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9

nusArpsCrpsEpriArplBsecY

rRNA16SrpsJrpsBruvBguaArplNserSrplFfrrrplArplErplCinfCrplDrplKpurAradAruvArpsMpyrHrplIrplMrpsGrpsLmraWrpsIttfrplStrmDtsfrplUrpsKrpsPrplOrplTrplVrpsSrplPrpsOsmpBrpsHrplQrplRrpsQrplLrpmAcoaE

Ribosomal protein Transcription/translation related proteinDNA repair protein Protein of other functionAMPHORA marker

Distance between the genome tree and 100 random trees (average ± standard deviation)

NODAL distance SPLIT distance

Distances between gene trees and the AMPHORA concatenated genome tree


Screen gene markers for any given taxonomic groupPhylogenetic group Genome

NumberGene Number

Maker Candidates

Archaea 62 145415 106

Actinobacteria 63 267783 136

Alphaproteobacteria 94 347287 121

Betaproteobacteria 56 266362 311

Gammaproteobacteria 126 483632 118

Deltaproteobacteria 25 102115 206

Epislonproteobacteria 18 33416 455

Bacteriodes 25 71531 286

Chlamydae 13 13823 560

Chloroflexi 10 33577 323

Cyanobacteria 36 124080 590

Firmicutes 106 312309 87

Spirochaetes 18 38832 176

Thermi 5 14160 974

Thermotogae 9 17037 684



0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

Alph

apro

teob

acteria

Betapr

oteo

bacter

ia

Gammap

roteob

acteria

Deltapr

oteo

bacter

ia

Epsil

onpr

oteo

bacter

ia

Uncla

ssified

Pro

teob

acteria

Cyan

obac

teria

Chlamyd

iae

Acidob

acteria

Bacter

oide

tes

Actin

obac

teria

Aquific

ae

Plan

ctom

ycetes

Spiro

chae

tes

Firmicu

tes

Chloro

flexi

Chloro

bi

Uncla

ssified

Bac

teria



Improves with better automation


Zorro

• http://sourceforge.net/projects/probmask/• ZORRO is a probabilistic masking program

that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines

• Wu, Chatterji, Eisen submitted


http://sourceforge.net/projects/probmask/

http://sourceforge.net/projects/probmask/

GEBA Phylogenomic Lesson 5

We have still only scratched the surface of microbial diversity


rRNA Tree of Life



Archaea

Eukaryotes

Bacteria


Phylogenetic Diversity: Sequenced Bacteria & Archaea

From Wu et al. 2009Tuesday, May 25, 2010



Phylogenetic Diversity with GEBA




Phylogenetic Diversity: Isolates




Phylogenetic Diversity: All

From Wu et al. 2009




Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter



• Most phyla with cultured species are sparsely sampled

• Lineages with no cultured taxa even more poorly sampled

Well sampled phylaPoorly sampled

No cultured taxaTuesday, May 25, 2010

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



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 phyla

Poorly sampled

No cultured taxaTuesday, May 25, 2010

Uncultured Lineages:Technical Approaches

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


GEBA Phylogenomic Lesson 6

Need Experiments from Across the Tree of Life too


Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter


As of 2002



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter


• Experimental studies are mostly from three phyla

As of 2002



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter


• Experimental studies are mostly from three phyla

• Some studies in other phyla

As of 2002



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Same trend in Eukaryotes

As of 2002



Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Same trend in Viruses

As of 2002



0.1

Acidobacteria

Bacteroides

Fibrobacteres

Gemmimonas

Verrucomicrobia

Planctomycetes

Chloroflexi

Proteobacteria

Chlorobi


Cyanobacteria

Chlamydia

Spriochaetes


Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter

Tree based on Hugenholtz (2002) with some modifications.

Need experimental studies from across the tree too


MICROBES


A Happy Tree of Life


Jonathan Eisen talk at ASM General Meeting 2010

Technology

Transcript of Jonathan Eisen talk at ASM General Meeting 2010