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Talk at ASBMB.
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A Phylogeny-Driven Genomic Encyclopedia of Bacteria and Archaea
Jonathan A. Eisen
Talk for ASBMBApril 25, 2010
Sunday, April 25, 2010
Eisen Lab - Phylogenomics of Novelty
Origin of New Functions and
Processes
Species Evolution
Genome Dynamics
•New genes•Changes in old genes•Changes in pathways
•Phylogenetic history•Vertical vs. horizontal descent•Needed to track gain/loss of processes, infer convergence
•Evolvability•Repair and recombination processes•Intragenomic variation
Sunday, April 25, 2010
Bacterial evolve
Sunday, April 25, 2010
Fleischmann et al. 1995TIGRTIGR
Sunday, April 25, 2010
Microbial genomes
From http://genomesonline.orgSunday, April 25, 2010
Sunday, April 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
Sunday, April 25, 2010
The Tree is not Happy
FIgure from Barton, Eisen et al. “Evolution”, CSHL Press.
Based on tree from Pace NR, 2003.
Archaea
Eukaryotes
Bacteria
Sunday, April 25, 2010
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
Sunday, April 25, 2010
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
Based on Hugenholtz, 2002
2002
Sunday, April 25, 2010
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
Based on Hugenholtz, 2002
2002
Sunday, April 25, 2010
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 ArchaeaBased on Hugenholtz, 2002
2002
Sunday, April 25, 2010
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 EukaryotesBased on Hugenholtz, 2002
2002
Sunday, April 25, 2010
Filling in the Genomic Phylogenetic Gaps
• 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
Sunday, April 25, 2010
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
• Solution I: sequence more phyla
• NSF-funded Tree of Life Project
• A genome from each of eight phyla
Eisen & Ward, PIs
Sunday, April 25, 2010
The Tree of Life is Still Angry
FIgure from Barton, Eisen et al. “Evolution”, CSHL Press.
Based on tree from Pace NR, 2003.
Eukaryotes
Bacteria
Archaea
Sunday, April 25, 2010
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
Sunday, April 25, 2010
From http://genomesonline.org
Microbial genomes 2010- ...
Sunday, April 25, 2010
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
Sunday, April 25, 2010
Why Increase Phylogenetic Coverage?
• Gene discovery• Annotation, functional prediction• Metagenomic analysis• Mechanisms of diversification• Species phylogeny and classification
Sunday, April 25, 2010
A Genomic Encyclopedia of Bacteria and Archaea (GEBA)
Sunday, April 25, 2010
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• Paper published in Nature Dec. 2009.
Sunday, April 25, 2010
GEBA Pilot Target List
0
5
10
15
20
25
30
35
B: A
ctinob
acteria
(High GC)
B: A
minan
aero
bia
B: A
quifica
e
B: B
actero
idetes
B: C
hlor
oflexi
B: D
efer
ribac
tere
s
B: D
efer
ribac
tere
s
B: D
eino
cocc
i
B: D
elta Pro
teob
acteria
B: Eps
ilon Pr
oteo
bacter
ia
B: Firm
icutes
B: Fus
obac
teria
B: G
amma Pr
oteo
bacter
ia
B: G
emmatim
onad
etes
B: H
aloa
naer
obiales
B: Planc
tomyc
etes
B: S
piro
chae
tes
B: The
rmod
esulfoba
cter
ia
B: The
rmod
esulfobia
B: The
rmov
enab
ulae
A: H
alob
acteria
A: A
rcha
eoglob
i
A: M
etha
noba
cter
ia
A: M
etha
nomicr
obia
A: The
rmoc
occi
A: The
rmop
rotei
Phyla
# o
f G
en
om
es
Sunday, April 25, 2010
GEBA and Openness
• All data being released as quickly as possible with no restrictions to IMG-GEBA; Genbank, etc
• Data also available in Biotorrents (http://biotorrents.net)
• Individual genome reports being published in new Open Access journal “Standards in Genome Sciences (SIGS)”
• Main GEBA paper in Nature freely available and published using Creative Commons License
Sunday, April 25, 2010
Assess Benefits of GEBA
• All genomes have some value
• But what, if any, is the benefit of tree-guided sequencing over other selection methods
• Lessons for other large scale microbial genome projects?
Sunday, April 25, 2010
GEBA Lesson 1
rRNA Tree is Useful for Identifying Phylogenetically Novel Genomes
rRNA Tree topology is not perfect;Genome-based trees better
Sunday, April 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
Sunday, April 25, 2010
Sunday, April 25, 2010
Network of Life
FIgure from Barton, Eisen et al. “Evolution”, CSHL Press.
Based on tree from Pace NR, 2003.
Archaea
Eukaryotes
Bacteria
Sunday, April 25, 2010
Wh
Whole genome tree built using AMPHORAby Martin Wu and Dongying Wu
Sunday, April 25, 2010
PD of rRNA, Genome Trees Similar
From Wu et al. 2009Sunday, April 25, 2010
Proteobacteria
Sunday, April 25, 2010
GEBA Lesson 2
Phylogenetically-guided genome selection improves genome
annotation
Sunday, April 25, 2010
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
Sunday, April 25, 2010
Most/All Functional Prediction Improves w/ Better Phylogenetic Sampling
• Better definition of protein family sequence “patterns”
• Conversion of hypothetical into conserved hypotheticals
• Greatly improves “comparative” and “evolutionary” based predictions
• Linking distantly related members of protein families
• Improved non-homology prediction
Sunday, April 25, 2010
From Wu et al. 2009.Sunday, April 25, 2010
GEBA Lesson 3
Improves analysis of genome data from uncultured organisms
Sunday, April 25, 2010
Metagenomics
shotgun
clone
Sunday, April 25, 2010
Sunday, April 25, 2010
rRNA phylotyping from metagenomics
Venter et al., 2004
Sunday, April 25, 2010
Shotgun Sequencing Allows Use of Alternative Anchors (e.g., RecA)
Venter et al., 2004
Sunday, April 25, 2010
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
Sunday, April 25, 2010
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
Cannot be done without good sampling of genomes
Sunday, April 25, 2010
ABCDEFG
TUVWXYZ
Binning challenge
Sunday, April 25, 2010
ABCDEFG
TUVWXYZ
Binning challenge
Best binning method: reference genomes
Sunday, April 25, 2010
ABCDEFG
TUVWXYZ
Binning challenge
No reference genome? What do you do?
Sunday, April 25, 2010
ABCDEFG
TUVWXYZ
Binning challenge
No reference genome? What do you do?
Phylogeny ....Sunday, April 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 treeSunday, April 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 tree
Cannot be done without good sampling of genomes
Sunday, April 25, 2010
GEBA Phylogenomic Lesson 5
We have still only scratched the surface of microbial diversity
Sunday, April 25, 2010
Protein Family Rarefaction Curves
• Take data set of multiple complete genomes• Identify all protein families using MCL• Plot # of genomes vs. # of protein families
Sunday, April 25, 2010
Sunday, April 25, 2010
Sunday, April 25, 2010
Sunday, April 25, 2010
Sunday, April 25, 2010
Sunday, April 25, 2010
MobileMotility
Element?
Sunday, April 25, 2010
Phylogenetic Distribution Novelty: Bacterial Actin Related Protein
Haliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam Zemla, Victor Kunin
!"#$%&'()*&& !"#$%&'(%()+"#,-.(/01 !"#*+,**'+(
2"#3)&4&*&& !"#*)$*),+%5"#$-.-6&0&1- !"#$%,$-%)(7"#0(1.8-9& !"#$''+-+,',!5"#:1,)*&$/0 !"#&$,%+)+-+
;"#01,&-*0 !"#%*+$--(<"#$-.-3.1%&0 !"#%',&'-+)
2"#$&*-.-1 !"#$'(-%%+&$="#$.1001 !"#-*$+$(&(>"#0$1,/%1.&0 !"#&$**+),)-!;"#01,&-*0 !"#*+,$*'(
5"#:1,)*&$/0 !"#&$,%+%-%%5"#$-.-6&0&1- !"#',&+$)*?"#@-%1*)A10(-. !"#&%'%&*%*B"#A1%%/0# "#%*,-&*'(2"#*-)').@1*0 !"#*-&'''(+5"#$-.-6&0&1- !"#',&&*&*?"#@-%1*)A10(-. !"#$)),)*%,;"#01,&-*0 !"#*+,$*),!;"#)$C.1$-/@ !"#&&),(*((-
."#,1(-*0 !"#$'-+*$((&!!"#(C1%&1*1 !"#$-,(%'+-!
5"#$-.-6&0&1- !"#$++-&%%!
?"#@-%1*)A10(-. !"#$)),),%)
?"#C1*0-*&&!"#&$-*$$(&$5"#$-.-6&0&1- !"#',&,$$%
5"#:1,)*&$/0 !"#&$,%+-,(,!5"#$-.-6&0&1- !"#$,+$(,&
?"#4&0$)&4-/@ !"#''-+&%$-
D"#01(&61 !"#$-&'*)%&+!!"#(C1%&1*1!"#$-%$ $),)
?"#@-%1*)A1(-. !"#$((&+,*-<"#@/0$/%/0 !"#&&'&%'*(,
((
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$++$++
'*
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See also Guljamow et al. 2007 Current Biology. Sunday, April 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
Sunday, April 25, 2010
Phylogenetic Diversity: Sequenced Bacteria & Archaea
From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html
Sunday, April 25, 2010
Phylogenetic Diversity with GEBA
From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html
Sunday, April 25, 2010
Phylogenetic Diversity: Isolates
From Wu et al. 2009.Sunday, April 25, 2010
Phylogenetic Diversity: All
From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html
Sunday, April 25, 2010
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 taxaSunday, April 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
Sunday, April 25, 2010
GEBA Phylogenomic Lesson 6
Need Experiments from Across the Tree of Life too
Sunday, April 25, 2010
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
Sunday, April 25, 2010
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
• Experimental studies are mostly from three phyla
As of 2002
Based on Hugenholtz, 2002
Sunday, April 25, 2010
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
• Experimental studies are mostly from three phyla
• Some studies in other phyla
As of 2002
Based on Hugenholtz, 2002
Sunday, April 25, 2010
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 Eukaryotes
As of 2002
Based on Hugenholtz, 2002
Sunday, April 25, 2010
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 Viruses
As of 2002
Based on Hugenholtz, 2002
Sunday, April 25, 2010
0.1
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
Tree based on Hugenholtz (2002) with some modifications.
Need experimental studies from across the tree too
Sunday, April 25, 2010
Sunday, April 25, 2010
MICROBES
Sunday, April 25, 2010
A Happy Tree of Life
Sunday, April 25, 2010
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)
Sunday, April 25, 2010