The Genomic Encyclopedia of Bacteria and Archaea & the Need for A Built Environment Culture Collection

A phylogeny driven genomic encyclopedia of bacteria and

archaea

Jonathan A. Eisen UC Davis

!

Culture Collection Meeting September 24, 2014

http://www.google.

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http://www.microbe.net/


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om/url?

GEBA

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

As of 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

As of 2002

Tree Based on Hugenholtz, 2002. http://genomebiology.com/2002/3/2/reviews/0003

http://genomebiology.com/2002/3/2/reviews/0003

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


• Genome sequences are mostly from three phyla

As of 2002



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



• Some other phyla are only sparsely sampled

As of 2002



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




As of 2002



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




As of 2002



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




• Solution I: sequence more phyla

• NSF-funded Tree of Life Project

• A genome from each of eight phyla

Eisen, Ward, Robb, Nelson, et al Tree Based on Hugenholtz,

2002. http://genomebiology.com/2002/3/2/reviews/0003


Saving Sequenced Strains

• Of 266 genomes done or in progress in 2011 • 138 were type strain for their species • 32 did not specify a strain • 123 in a public culture collection

Nature. 2001 Nov 8;414(6860):148.

Saving Sequenced StrainsWe propose that the following standards should be adopted by the entire community. First, genome-sequencing project lists and databases should include the name of the strain sequenced and its associated culture collection accession number(s), as well as its origin. Second, the type strain of a species should be used for sequencing unless other factors make this inappropriate. Third, strains for which genome sequences have been, or are being, generated should be deposited in at least two major public biological resource centres, such as the American Type Culture Collection, the German Collection of Microorganisms and Cell Cultures, the Pasteur Institute Collection or the Japanese Collection of Microorganisms.

Saving Sequenced StrainsRecommended Policy: !

Order strains for sequencing from Culture Collections to guarantee one is using a strain that is available to others !

If new project, first deposit strains in collection and then re-obtain them from collection.

Phylum

Species selected

Chrysiogenes

Chrysiogenes arsenatis (GCA)

Coprothermobacter

Coprothermobacter proteolyticus (GCBP)

Dictyoglomi

Dictyoglomus thermophilum (GD T )

Thermodesulfobacteria

Thermodesulfobacterium commune (GTC)

Nitrospirae

Thermodesulfovibrio yellowstonii (GTY)

Thermomicrobia

Thermomicrobium roseum (GTR )

Deferribacteres

Geovibrio thiophilus (GGT)

Synergistes

Synergistes jonesii (GSJ)

Organisms Selected

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




• Still highly biased in terms of the tree



Eisen & Ward, PIs Tree Based on Hugenholtz, 2002. http://genomebiology.com/2002/3/2/reviews/0003


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

Deinococcus-Thermus

Aquificae

Thermotogae

TM6OS-K

Termite GroupOP8

Marine GroupAWS3

OP9

NKB19

OP3

OP10

TM7

OP1OP11

Nitrospira



Chrysiogenetes

Thermomicrobia

Dictyoglomus

Coprothmermobacter




• Same trend in Archaea





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




• Same trend in Eukaryotes





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




• Same trend in Viruses








• Solution: Really Fill in the Trees

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



Filling in the Tree

Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree


Filling in the Tree


Filling in the Tree


Filling in the Tree

Lots of Plants, Animals, Fungi


Exclude Plants, Animals, Fungi


A Genomic Encyclopedia of Microbes (GEM)


Just Say No to Eukaryotes


GEBA: A Genomic Encyclopedia of Bacteria and Archaea


GEBA

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

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)

Lesson 1: rRNA PD IDs novel lineages

From Wu et al. 2009 Nature 462, 1056-1060

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

Lesson 2: rRNA Tree is not perfect

Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.

16s WGT, 23S

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15879228&query_hl=2

Lesson 3: Improves Analysis

Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.


Synapomorphies exist

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

Lesson 9: Improves metagenomicsSargasso Phylotypes

Wei

ghte

d %

of C

lone

s

0.000

0.125

0.250

0.375

0.500

Major Phylogenetic Group

Alphapro

teobacteria

Betap

roteobacteria

Gamm

aproteobacteria

Epsilo

nproteobacteria

Deltapro

teobacteria

Cyanobacteria

Firmicutes

Actinobacteria

Chlorobi

CFB

Chloroflexi

Spirochaetes

Fusobacteria

Deinococcus-Th

ermus

Euryarchaeota

Crenarchaeota

EFG EFTu HSP70RecA RpoB rRNA

Venter et al., Science 304: 66-74. 2004

GEBA Project improves metagenomic analysis


Lesson 4 : Metadata & Data Papers

Lesson 5: Project management critical

• Tracking samples and status • Getting permissions • Shipping samples • Contacting collaborators • Data archiving and submission • Communicating with core facilities • and more

Lesson 6: Culture Collections Needed

GEBA Biggest Challenge: Getting DNA

• Getting quality DNA is biggest bottleneck • Solution: Beg Borrow and Steal !

• DSMZ offered to do for free • ATCC is doing a small number for a fee • In discussions with other PCC and other

collections

MicroorganismsQuantification gel of the genomic DNA isolated from Conexibacter woesei (DSM 14684T)

Conexibacter woesei (DSM 14684T) was taken from the German Collection of Microorganisms and Cell Cultures (DSMZ). The genomic DNA was isolated using the Qiagen Genomic 500 DNA Kit (Qiagen 10262). The genomic DNA was 10-250 kb in size as determined by Pulsed Field Gel Electrophoresis (PFGE). The bulk of DNA had a size of 50-250 kb (see attached PFGE image). The DNA concentration is 500 ng/µl as estimated from the gel. Spectrophotometric measurements yielded a DNA concentration of 450 µg/ml; 300 µl of genomic DNA are shipped (150 µg).

1 2 3 4 5 6 7 8

Lane 1: c(λ-Marker)= 15 ng Lane 2: c(λ-Marker)= 30 ng Lane 3: c(λ-Marker)= 50 ng Lane 4: DNA Molecular Weight Marker II (Roche 236250) Lane 5: DSM 13279, Collinsella stercoris Lane 6: DSM 43043, Intrasporangium calvum Lane 7: DSM 18053, Dyadobacter fermentans Lane 8: DSM 20476, Slackia heliotrinireducens

Lane 9: DSM 18081, Patulibacter minatonensis Lane 10: DSM 14684, Conexibacter woesei Lane 11: DSM 11002, Dethiosulfovibrio peptidovorans Lane 12: DSM 11551, Halogeometricum borinquense Lane 13: DNA Molecular Weight Marker II (Roche 236250) Lane 14: c(λ-Marker)= 125 ng Lane 15: c(λ-Marker)= 250 ng Lane 16: c(λ-Marker)= 500 ng

9 10 11 12 13 14 15 16

GEBA Cyanobacteria

www.pnas.org/cgi/doi/10.1073/pnas.1217107110

Haloarchaeal GEBA-like

Lynch EA, Langille MGI, Darling A, Wilbanks EG, Haltiner C, et al. (2012) Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux. PLoS ONE 7(7): e41389. doi:10.1371/journal.pone.0041389

49

Plan: Sequence multiple Root Nodule Bacteria (RNBs) across the

planet. Pilot: 100 RNBs.

Alpha RNB

BradyrhizobiumMesorhizobiumRhizobium

Beta RNB

Sinorhizobium

CupriavidisBurkholderia

Balneimonas-like

DevosiaOchrobactrumPhyllobacterium

AzorhizobiumAllorhizobium

Goal: • Understand BioGeographical effects on species

evolution and understand host-specificity.

Rationale: • N2 fixation by legume pastures and crops provides 65% of the

N currently utilized in agricultural production. • Contributes 25 to 90 million metric tones N pa.

• Symbioses save $US 6-10 billion annually on N fertilizer.

• Grain and animal production enhanced by fixed nitrogen supplied by the symbiosis.

Nikos Kyrpides

GEBA RNB

Future?

Future 1: Massive Diversity

From Wu et al. 2009 Nature 462, 1056-1060


JGI Dark Matter Project

environmental samples (n=9)

isolation of singlecells (n=9,600)

whole genomeamplification (n=3,300)

SSU rRNA gene based identification

(n=2,000)

genome sequencing, assembly and QC (n=201)

draft genomes(n=201)

SAK

HSM ETLTG

HOT

GOM

GBS

EPR

TAETL T

PR

EBS

AK E

SM G TATTG

OM

OT

seawater brackish/freshwater hydrothermal sediment bioreactor

GN04WS3 (Latescibacteria)GN01

!"#$%&'$LD1

WS1PoribacteriaBRC1

LentisphaeraeVerrucomicrobia

OP3 (Omnitrophica)ChlamydiaePlanctomycetes

NKB19 (Hydrogenedentes)WYOArmatimonadetesWS4

ActinobacteriaGemmatimonadetesNC10SC4WS2

Cyanobacteria()*&2

Deltaproteobacteria

EM19 (Calescamantes)+,-*./'&'012345678#89/,-568/:

GAL35Aquificae

EM3Thermotogae

Dictyoglomi

SPAMGAL15

CD12 (Aerophobetes)OP8 (Aminicenantes)AC1SBR1093

ThermodesulfobacteriaDeferribacteres

Synergistetes

OP9 (Atribacteria)()*&2

CaldisericaAD3

Chloroflexi

AcidobacteriaElusimicrobiaNitrospirae49S1 2B

CaldithrixGOUTA4

*;<%0123=/68>8?8,6@98/:Chlorobi

486?8,A-5BTenericutes4AB@9/,-568/Chrysiogenetes

Proteobacteria

4896@9/,-565BTG3SpirochaetesWWE1 (Cloacamonetes)

C=1ZB3

=D)&'EF58>@,@,,AB&CG56?ABOP1 (Acetothermia)Bacteriodetes

TM7GN02 (Gracilibacteria)

SR1BH1

OD1 (Parcubacteria)

(*1OP11 (Microgenomates)

Euryarchaeota

Micrarchaea

DSEG (Aenigmarchaea)Nanohaloarchaea

Nanoarchaea

Cren MCGThaumarchaeota

Cren C2Aigarchaeota

Cren pISA7

Cren ThermoproteiKorarchaeota

pMC2A384 (Diapherotrites)

BACTERIA ARCHAEA

archaeal toxins (Nanoarchaea)

lytic murein transglycosylase

stringent response (Diapherotrites, Nanoarchaea)

ppGpp

limitingamino acids

SpotT RelA

(GTP or GDP)+ PPi

GTP or GDP+ATP

limitingphosphate,fatty acids,carbon, iron

DksA

Expression of components for stress response

sigma factor (Diapherotrites, Nanoarchaea)

!4

"#$#"%

!2!3 !1

-35 -10

&'()

&*()

+',#-./0123452

oxidoretucase

+ +e- donor e- acceptor

H

'Ribo

ADP

+

'62

O

Reduction

OxidationH

'Ribo

ADP

'6

O

2H

',)##$#6##$#72#####################',)6+ + -

HGT from Eukaryotes (Nanoarchaea)

Eukaryota

O68*62

OH

'6

*8*63

OO

68*62

'6

*8*63

O

tetra-peptide

O68*62

OH

'6

*8*63

OO

68*62

'6

*8*63

O

tetra-peptide

murein (peptido-glycan)

archaeal type purine synthesis (Microgenomates)

PurFPurD9:3'PurL/QPurMPurKPurE9:3*PurB

PurP

?

Archaea

adenine guanine

O

6##'2

+'

'62

'

'

H

H

'

'

'

H

HH' '

H

PRPP ;,<*,+

IMP

,<*,+

A*

GUA *G U

GU

A

*

GU

A UA * U

A * U

Growing AA chain

=+',>?/0@#recognizes

UGA1+',

UGA recoded for Gly (Gracilibacteria)

ribosome

Woyke et al. Nature 2013.


Future 2: Eukaryotes and Viruses


A Genomic Encyclopedia of Microbes (GEM)


Future 3

• Need Experiments from Across the Tree of Life too

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


As of 2002



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


• Experimental studies are mostly from three phyla

As of 2002



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


• 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

Deinococcus-Thermus

Aquificae

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

Deinococcus-Thermus

Aquificae

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

Deinococcus-Thermus

Aquificae

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



0.1

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

Tree based on Hugenholtz (2002) with some modifications.

Adopt a Microbe



http://www.google.

com/



om/url?

