a phylogeny driven genomic encyclopedia of bacteria and archaea
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A phylogeny driven genomic encyclopedia of bacteria and archaea
Jonathan A. Eisen
Talk at Stanford UniversityApril 17, 2010
Saturday, April 24, 2010
Bacterial evolve
Saturday, April 24, 2010
Fleischmann et al. 1995
Saturday, April 24, 2010
Microbial genomes
From http://genomesonline.orgSaturday, April 24, 2010
Saturday, April 24, 2010
rRNA Tree of Life
Based on tree by
Norm Pace
Saturday, April 24, 2010
The Tree is not Happy
Based on tree by
Norm Pace
Saturday, April 24, 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
Saturday, April 24, 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
As of 2002
Based on Hugenholtz, 2002
Saturday, April 24, 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
As of 2002
Based on Hugenholtz, 2002
Saturday, April 24, 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 Archaea
As of 2002
Based on Hugenholtz, 2002
Saturday, April 24, 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
Saturday, April 24, 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
Saturday, April 24, 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
Saturday, April 24, 2010
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
Saturday, April 24, 2010
Bacterial aTOL Project AIMS
• Improve resolution of deep branches in the bacterial tree
• Launch biological studies of these phyla
• Leverage data for interpreting environmental surveys
Saturday, April 24, 2010
T. roseum genome
Saturday, April 24, 2010
From http://genomesonline.org
Microbial genomes
Saturday, April 24, 2010
The Tree of Life is Still Angry
Saturday, April 24, 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
Saturday, April 24, 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
Saturday, April 24, 2010
http://www.jgi.doe.gov/programs/GEBA/pilot.htmlSaturday, April 24, 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
Saturday, April 24, 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
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B: D
efer
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B: D
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B: D
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B: D
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B: Eps
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bacter
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B: Firm
icutes
B: Fus
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teria
B: G
amma Pr
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bacter
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B: G
emmatim
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etes
B: H
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B: Planc
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B: S
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chae
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B: The
rmod
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cter
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B: The
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rmov
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alob
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Phyla
# o
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es
Saturday, April 24, 2010
Why Increase Taxonomic Coverage?
• Gene discovery• Annotation, functional prediction• Metagenomic analysis• Mechanisms of diversification• Species phylogeny and classification
Saturday, April 24, 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)
Saturday, April 24, 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?
Saturday, April 24, 2010
GEBA Lesson 1
rRNA Tree is Useful for Identifying Phylogenetically Novel Genomes
rRNA Tree topology is not perfect;Genome-based trees better
Saturday, April 24, 2010
rRNA Tree of Life
Based on tree by
Norm Pace
Saturday, April 24, 2010
Saturday, April 24, 2010
Saturday, April 24, 2010
Wh
Whole genome tree built using AMPHORAby Martin Wu and Dongying Wu
Saturday, April 24, 2010
PD of rRNA, Genome Trees Similar
From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html
Saturday, April 24, 2010
Proteobacteria
Saturday, April 24, 2010
GEBA Lesson 2
Phylogenetically-guided genome selection improves genome
annotation
Saturday, April 24, 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
Saturday, April 24, 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
Saturday, April 24, 2010
From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html
Saturday, April 24, 2010
GEBA Lesson 3
Improves analysis of genome data from uncultured organisms
Saturday, April 24, 2010
Environmental Shotgun Sequencing
shotgun
clone
Saturday, April 24, 2010
Saturday, April 24, 2010
rRNA phylotyping from metagenomics
Venter et al., 2004
Saturday, April 24, 2010
Shotgun Sequencing Allows Use of Alternative Anchors (e.g., RecA)
Venter et al., 2004
Saturday, April 24, 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
Saturday, April 24, 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
Saturday, April 24, 2010
ABCDEFG
TUVWXYZ
Binning challenge
Saturday, April 24, 2010
ABCDEFG
TUVWXYZ
Binning challenge
Best binning method: reference genomes
Saturday, April 24, 2010
ABCDEFG
TUVWXYZ
Binning challenge
No reference genome? What do you do?
Saturday, April 24, 2010
ABCDEFG
TUVWXYZ
Binning challenge
No reference genome? What do you do?
Phylogeny ....Saturday, April 24, 2010
Phylogenetic Binning Using AMPHORA
0
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0.2
0.3
0.4
0.5
0.6
0.7
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roteob
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dnaGfrrinfCnusApgkpyrGrplArplBrplCrplDrplErplFrplKrplLrplMrplNrplPrplSrplTrpmArpoBrpsBrpsCrpsErpsIrpsJrpsKrpsMrpsSsmpBtsf
AMPHORA - each read on its own treeSaturday, April 24, 2010
Phylogenetic Binning Using AMPHORA
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
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apro
teob
acteria
Betapr
oteo
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ia
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roteob
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AMPHORA - each read on its own tree
Cannot be done without good sampling of genomes
Saturday, April 24, 2010
GEBA Phylogenomic Lesson 5
We have still only scratched the surface of microbial diversity
Saturday, April 24, 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
Saturday, April 24, 2010
Saturday, April 24, 2010
Saturday, April 24, 2010
Saturday, April 24, 2010
Saturday, April 24, 2010
Saturday, April 24, 2010
Phylogenetic Distribution Novelty: Bacterial Actin Related Protein
Haliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam Zemla, Victor Kunin
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From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.htmlSaturday, April 24, 2010
rRNA Tree of Life
Based on tree by
Norm Pace
Saturday, April 24, 2010
Phylogenetic Diversity: Sequenced Bacteria & Archaea
From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html
Saturday, April 24, 2010
Phylogenetic Diversity with GEBA
From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html
Saturday, April 24, 2010
Phylogenetic Diversity: Isolates
From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.htmlSaturday, April 24, 2010
Phylogenetic Diversity: All
From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html
Saturday, April 24, 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 taxaSaturday, April 24, 2010
Uncultured Lineages:Technical Approaches
• Get into culture• Enrichment cultures• If abundant in low diversity ecosystems• Flow sorting• Microbeads• Microfluidic sorting• Single cell amplification
Saturday, April 24, 2010
GEBA Phylogenomic Lesson 6
Need Experiments from Across the Tree of Life too
Saturday, April 24, 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
Saturday, April 24, 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
Saturday, April 24, 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
Saturday, April 24, 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
Saturday, April 24, 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
Saturday, April 24, 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
Saturday, April 24, 2010
Saturday, April 24, 2010
MICROBES
Saturday, April 24, 2010
A Happy Tree of Life
Saturday, April 24, 2010
Lateral transfer
• Many lines of evidence suggest it is important in adaptations in microbes– E.g., K12 vs. O157:H7– e.g., Many genes show anomalous patterns
• However, does not appear to wipe out phylogenetic signal– Core of genomes gives similar phylogeny– Most acquired genes do not last long in lineages– Many claims of LGT are more “identification of
anomalies” than detecting LGT
Saturday, April 24, 2010
Saturday, April 24, 2010
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