Talk by Jonathan Eisen on "A genomic encyclopedia of bacteria and archaea" at Lake Arrowhead Small Genomes meeting in 2008.

1. A Genomic Encyclopedia of
Bacteria and Archaea
(GEBA)
Jonathan A. Eisen
U. C. Davis and J. G. I.
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2. Outline
• Background
– Why history matters
– Gaps in available genomes
• The GEBA pilot project
• Future needs
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3. The Tree of Life
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4. Famous Arrowhead 2004 Quotes
• Space-time continuum of genes and genomes
• Gene sequences are the wormhole that allows
one to tunnel into the past
• The human mind can conceive of things with
no basis in physical reality
• Thoughts can go faster than the speed of light
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5. Famous Arrowhead Quotes 2006
• Publications, student degrees, etc.
• Not trying to say anything bad about
anyone
• The human guts are a real milieu
• Where’s you evening gown?
• You better kiss everybody
• This is how you do metagenomics on 50
dollars, and that’s Canadian dollars
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6. QuickTime™ and a
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8. Major Microbial Sequencing Efforts
• Coordinated, top-down efforts
– Fungal Genome Initiative (Broad/Whitehead)
– Gordon and Betty Moore Foundation Marine Microbial Genome
Sequencing Project
– Sanger Center Pathogen Sequencing Unit
– NHGRI Human Gut Microbiome Project
– NIH Human Microbiome Program
• White paper or grant systems
– NIAID Microbial Sequencing Centers
– DOE/JGI Community Sequencing Program
– DOE/JGI BER Sequencing Program
– NSF/USDA Microbial Genome Sequencing
• Covers lots of ground and biological diversity
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9. The Tree of Life
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10. The Tree is not Happy
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11. As of 2002 Proteobacteria
TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Bacteroides bacteria
Chlorobi
Fibrobacteres
Marine GroupA
WS3
Gemmimonas
Firmicutes
Fusobacteria
Actinobacteria
OP9
Cyanobacteria
Synergistes
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroflexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquificae
Thermudesulfobacteria
Thermotogae
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Hugenholtz, 2002
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12. As of 2002 Proteobacteria
TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Bacteroides
bacteria
Chlorobi
Fibrobacteres
Marine GroupA • Genome
WS3
Gemmimonas
Firmicutes
sequences are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria three phyla
Synergistes
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroflexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquificae
Thermudesulfobacteria
Thermotogae
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Hugenholtz, 2002
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13. As of 2002 Proteobacteria
TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Bacteroides
bacteria
Chlorobi
Fibrobacteres
Marine GroupA • Genome
WS3
Gemmimonas
Firmicutes
sequences are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria three phyla
Synergistes
Deferribacteres
Chrysiogenetes • Some other
NKB19
Verrucomicrobia
Chlamydia phyla are
OP3
Planctomycetes
Spriochaetes
only sparsely
Coprothmermobacter
OP10 sampled
Thermomicrobia
Chloroflexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquificae
Thermudesulfobacteria
Thermotogae
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14. As of 2002 Proteobacteria
TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Bacteroides
bacteria
Chlorobi
Fibrobacteres
Marine GroupA
• Genome
WS3
Gemmimonas sequences are
Firmicutes
Fusobacteria mostly from
Actinobacteria
OP9
Cyanobacteria
three phyla
Synergistes
Deferribacteres
Chrysiogenetes
• Some other
NKB19
Verrucomicrobia
Chlamydia
phyla are
OP3
Planctomycetes only sparsely
Spriochaetes
Coprothmermobacter
OP10
sampled
Thermomicrobia
Chloroflexi
TM7
• Same trend in
Deinococcus-Thermus
Dictyoglomus
Aquificae
Archaea,
Thermudesulfobacteria
Thermotogae Eukaryotes
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15. Need for Tree Guidance Well Established
• Common approach within some eukaryotic groups
– NHGRI animal projects
– FGI at Whitehead
– Plant sequencing at JGI
• Phylogenetic gaps in bacterial and archaeal projects
commonly lamented in literature
• Many small projects funded to fill in some gaps
– DOE/TIGR Sequencing
– Multiple CSP projects
– Multiple NSF/USDA projects
– Private projects (e.g., Integrated Genomics, Diversa)
– TIGR (Eisen, Ward) Bacterial Tree of Life Project
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16. Why Increase Taxonomic Coverage?
• Mechanisms of diversification
• Gene discovery
• Annotation, functional prediction
• Metagenomic analysis
• Species phylogeny and classification
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17. Proteobacteria
• Eisen-Ward TM6 • At least 40
OS-K
NSF Tree of Acidobacteria
Termite Group phyla of
OP8
Life Project Nitrospira
Bacteroides
bacteria
Chlorobi
• A genome Fibrobacteres
Marine GroupA
• Genome
WS3
from each of Gemmimonas sequences are
Firmicutes
eight phyla Fusobacteria mostly from
Actinobacteria
OP9
Cyanobacteria
three phyla
Synergistes
Deferribacteres
Chrysiogenetes
• Some other
NKB19
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Verrucomicrobia
Chlamydia
phyla are only
OP3
Planctomycetes sparsely
Spriochaetes
Coprothmermobacter
OP10
sampled
Thermomicrobia
Based on Chloroflexi
TM7
• Solution I:
Hugenholtz, Deinococcus-Thermus
Dictyoglomus sequence more
2002 Aquificae
Thermudesulfobacteria
Thermotogae phyla
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18. The Tree of Life is Still Angry
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19. Within Phyla Diversity Immense
• Each phyla represents billions of years of
evolution
• Some have hundreds of major lineages,
most with no genomes
• Need to sample within phyla too
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20. Major Lineages of Actinobacteria
2.5.1 Acidimicrobidae
2.5.1.1 Unclassified
2.5.1.2 "Microthrixineae
2.5.1.3 Acidimicrobineae
2.5.1.4 BD2-10
2.5.1.5 EB1017
2.5.2 Actinobacteridae
2.5.2.1 Unclassified
2.5.2.10 Ellin306/WR160
2.5.2.11 Ellin5012
2.5.2.12 Ellin5034
2.5.2.13 Frankineae
2.5.2.14 Glycomyces
2.5.2.15 Intrasporangiaceae
2.5.2.16 Kineosporiaceae
2.5.2.17 Microbacteriaceae
2.5.2.18 Micrococcaceae
2.5.2.19 Micromonosporaceae
2.5.2.2 Actinomyces
2.5.2.20 Propionibacterineae
2.5.2.21 Pseudonocardiaceae
2.5.2.22 Streptomycineae
2.5.2.23 Streptosporangineae
2.5.2.3 Actinomycineae
2.5.2.4 Actinosynnemataceae
2.5.2.5 Bifidobacteriaceae
2.5.2.6 Brevibacteriaceae
2.5.2.7 Cellulomonadaceae
2.5.2.8 Corynebacterineae
2.5.2.9 Dermabacteraceae
2.5.3 Coriobacteridae
2.5.3.1 Unclassified
2.5.3.2 Atopobiales
2.5.3.3 Coriobacteriales
2.5.3.4 Eggerthellales
2.5.4 OPB41
2.5.5 PK1
2.5.6 Rubrobacteridae
2.5.6.1 Unclassified
2.5.6.2 "Thermoleiphilaceae QuickTime™ and a
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2.5.6.4 Rubrobacteraceae

21. Major Lineages of Actinobacteria II
2.5 Actinobacteria
2.5.1 Acidimicrobidae
2.5.1.1 Unclassified
2.5.1.2 "Microthrixineae
2.5.1.3 Acidimicrobineae
2.5.1.3.1 Unclassified
2.5.1.3.2 Acidimicrobiaceae
2.5.1.4 BD2-10
2.5.1.5 EB1017
2.5.2 Actinobacteridae
2.5.2.1 Unclassified
2.5.2.10 Ellin306/WR160
2.5.2.11 Ellin5012
2.5.2.12 Ellin5034
2.5.2.13 Frankineae
2.5.2.13.1 Unclassified
2.5.2.13.2 Acidothermaceae
2.5.2.13.3 Ellin6090
2.5.2.13.4 Frankiaceae
2.5.2.13.5 Geodermatophilaceae
2.5.2.13.6 Microsphaeraceae
2.5.2.13.7 Sporichthyaceae
2.5.2.14 Glycomyces
2.5.2.15 Intrasporangiaceae
2.5.2.15.1 Unclassified
2.5.2.15.2 Dermacoccus
2.5.2.15.3 Intrasporangiaceae
2.5.2.16 Kineosporiaceae
2.5.2.17 Microbacteriaceae
2.5.2.17.1 Unclassified
2.5.2.17.2 Agrococcus
2.5.2.17.3 Agromyces
2.5.2.18 Micrococcaceae
2.5.2.19 Micromonosporaceae
2.5.2.2 Actinomyces
2.5.2.20 Propionibacterineae
2.5.2.20.1 Unclassified
2.5.2.20.2 Kribbella
2.5.2.20.3 Nocardioidaceae
2.5.2.20.4 Propionibacteriaceae
2.5.2.21 Pseudonocardiaceae
2.5.2.22 Streptomycineae
2.5.2.22.1 Unclassified
2.5.2.22.2 Kitasatospora
2.5.2.22.3 Streptacidiphilus
2.5.2.23 Streptosporangineae
2.5.2.23.1 Unclassified
2.5.2.23.2 Ellin5129
2.5.2.23.3 Nocardiopsaceae
2.5.2.23.4 Streptosporangiaceae
2.5.2.23.5 Thermomonosporaceae
2.5.2.3 Actinomycineae
2.5.2.4 Actinosynnemataceae
2.5.2.5 Bifidobacteriaceae
2.5.2.6 Brevibacteriaceae
2.5.2.7 Cellulomonadaceae
2.5.2.8 Corynebacterineae
2.5.2.8.1 Unclassified
2.5.2.8.2 Corynebacteriaceae
2.5.2.8.3 Dietziaceae
2.5.2.8.4 Gordoniaceae
2.5.2.8.5 Mycobacteriaceae
2.5.2.8.6 Rhodococcus
2.5.2.8.7 Rhodococcus
2.5.2.8.8 Rhodococcus
2.5.2.9 Dermabacteraceae
2.5.2.9.1 Unclassified
2.5.2.9.2 Brachybacterium
2.5.2.9.3 Dermabacter
2.5.3 Coriobacteridae
2.5.3.1 Unclassified
2.5.3.2 Atopobiales
2.5.3.3 Coriobacteriales
2.5.3.4 Eggerthellales
2.5.4 OPB41
2.5.5 PK1
2.5.6 Rubrobacteridae
2.5.6.1 Unclassified
2.5.6.2 "Thermoleiphilaceae
2.5.6.2.1 Unclassified
2.5.6.2.2 Conexibacter
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22. Proteobacteria
TM6
OS-K
• At least 100 phyla of
Acidobacteria
Termite Group bacteria
OP8
Nitrospira
Bacteroides • Genome sequences are
Chlorobi
Fibrobacteres
Marine GroupA mostly from three phyla
WS3
Gemmimonas
Firmicutes
• Most phyla with cultured
Fusobacteria
Actinobacteria
species are sparsely
OP9
Cyanobacteria
Synergistes
sampled
Deferribacteres
Chrysiogenetes
NKB19
• Lineages with no cultured
Verrucomicrobia
Chlamydia
OP3
taxa even more poorly
Planctomycetes
Spriochaetes sampled
Coprothmermobacter
OP10
Thermomicrobia • Solution - use tree to really
Chloroflexi
TM7
Deinococcus-Thermus
fill gaps
Dictyoglomus
Aquificae
Well sampled phyla
Thermudesulfobacteria
Thermotogae
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23. QuickTime™ and a
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24. GEBA Pilot Project: Components
• Project management (David Bruce, Lynne Goodwin et al)
• Selection of strains (Phil Hugenholtz, Nikos Kyrpides,
Jonathan Eisen)
• Culture collection and DNA prep (DSMZ, Hans-Peter
Klenk)
• Libraries and DNA (Eileen Dalin et al.)
• Sequencing and closure (Susan Lucas, Alla Lapidus et al.)
• Annotation and database needs (Nikos Kyrpides)
• Analysis (Dongying Wu, Martin Wu, Jenna Morgan,
Victor Kunin, Marcel Huntemann, Neil Rawlings, Ian
Paulsen, Gary Xie, Patrick Chain, Patrik D’Haeseleer,
Sean Hooper, Iain Anderson, Mavrommatis Kostas)
• Adopt a microbe education project (Cheryl Kerfeld)
• Outreach (David Gilbert)
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25. GEBA Pilot I:
Identifying Lineages without
Genomes
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28. QuickTime™ and a
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29. GEBA Pilot II:
Selecting Targets
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30. Key Criteria
• Phylogenetic novelty
– Working from top of tree down
– Also selected one phylum to fill in in more detail -
Actinobacteria
• Culturable
– Type strain preferred is all else equal
• DOE mission relevance
• Ready availability to us and community
– Of strain
– Of DNA
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31. GEBA Pilot III:
Partnership with DSMZ
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32. GEBA Biggest Challenge:
Getting DNA
• Getting quality DNA is biggest bottleneck
• Decided to test as part of the GEBA pilot
the possibility of getting DNA directly from
culture collections
• DSMZ offered to do for free
• ATCC is doing a small number for a fee
• Working with other culture collections
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34. Quantification gel of the genomic DNA isolated from Microorganisms
Microorganisms
Conexibacter woesei (DSM 14684T)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
Lane 1: c(λ-Marker)= 15 ng Lane 9: DSM 18081, Patulibacter minatonensis
Lane 2: c(λ-Marker)= 30 ng Lane 10: DSM 14684, Conexibacter woesei
Lane 3: c(λ-Marker)= 50 ng Lane 11: DSM 11002, Dethiosulfovibrio peptidovorans
Lane 4: DNA Molecular Weight Marker II (Roche Lane 12: DSM 11551, Halogeometricum borinquense
236250) Lane 13: DNA Molecular Weight Marker II (Roche
Lane 5: DSM 13279, Collinsella stercoris 236250)
Lane 6: DSM 43043, Intrasporangium calvum Lane 14: c(λ-Marker)= 125 ng
Lane 7: DSM 18053, Dyadobacter fermentans Lane 15: c(λ-Marker)= 250 ng
Lane 8: DSM 20476, Slackia heliotrinireducens Lane 16: c(λ-Marker)= 500 ng
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
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35. GEBA Pilot IV:
Sequencing Progress
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37. GEBA Pilot Target List
35
30
25
20
15
# of Genomes
10
5
0
B: Aquificae
B: Chloroflexi Deinococci Firmicutes
B: B:
B: Bacteroidetes B: Fusobacteria B: Spirochaetes Halobacteria Thermococci
A: A: Archaeoglobi Thermoprotei
A: A:
B: AminanaerobiaDeferribacteres
B: B: Deferribacteres B: Planctomycetes A: Methanobacteria
B: Haloanaerobiales Thermovenabulae
B: Thermodesulfobia Methanomicrobia
B: A:
B: Gemmatimonadetes
B: Delta Proteobacteria
B: Epsilon B: Gamma Proteobacteria
Proteobacteria B: Thermodesulfobacteria
B: Actinobacteria (High GC)
Phyla
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38. GEBA Pilot Status 5-12-08
35
30
25
Closed
20
Post Draft
Production
15 Library
Awaiting Material
# of Genomes
10
5
0
B: Aquificae B: Firmicutes
B: Chloroflexi
B: Deinococci
B: Bacteroidetes A: HalobacteriaA:
A: Thermococci
B: Fusobacteria B: Spirochaetes A: ArchaeoglobiThermoprotei
B: Aminanaerobia Deferribacteres
B: Deferribacteres
B: B: Planctomycetes
B: Haloanaerobiales A: A: Methanomicrobia
Methanobacteria
B: Thermodesulfobia
B: Thermovenabulae
B: Gemmatimonadetes
B: Delta Proteobacteria
B: Epsilon Proteobacteria B: Thermodesulfobacteria
B: Gamma Proteobacteria
B: Actinobacteria (High GC)
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39. Non Active Projects
16
14
12
10
Abandoned
8 On Hold
# of6Genomes
4
2
0
B: Aquificae
B: ChloroflexiDeinococciFirmicutes
B: B:
B: Bacteroidetes B: Fusobacteria B: Spirochaetes Halobacteria A: Thermoprotei
A: A: Archaeoglobi
A: Thermococci
B: Aminanaerobia Deferribacteres
B: Deferribacteres
B: B: Planctomycetes A: Methanobacteria
B: HaloanaerobialesThermovenabulae
B: ThermodesulfobiaMethanomicrobia
B: A:
B: Gemmatimonadetes
B: Delta Proteobacteria
B: EpsilonB: Gamma Proteobacteria
Proteobacteria B: Thermodesulfobacteria
B: Actinobacteria (High GC)
Phyla
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40. GEBA Pilot Data Release
30
25
20
15
# of Genomes
10
5
0
B: Aquificae
B: Chloroflexi Deinococci Firmicutes
B: B:
B: Bacteroidetes B: Fusobacteria B: Spirochaetes A: Halobacteria A: Thermococci
A: Archaeoglobi A: Thermoprotei
B: Aminanaerobia Deferribacteres
B: B: Deferribacteres B: Planctomycetes A: Methanobacteria
B: HaloanaerobialesB: Thermovenabulae
B: Thermodesulfobia A: Methanomicrobia
B: Delta Proteobacteria Gemmatimonadetes
B:
B: Epsilon Proteobacteria B: Thermodesulfobacteria
B: Gamma Proteobacteria
B: Actinobacteria (High GC)
Phyla
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41. Progress Report
GEBA Status 5-12-08
Closed
3%
Awaiting Material
26%
Post Draft
51%
Library
9%
Production
11%
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42. Progress
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43. Data
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44. Organism Domain Phylum Status IMG-GEBA NCBI-PID Culture-ID GOLD-ID
Acidimicrobium ferrooxidans DSM 10331 Bacteria Actinobacteria draft 2500645360 29525 DSM 10331 Gi02326
Actinosynnema mirum 101, DSM 43827 Bacteria Actinobacteria draft 2500395345 19705 DSM 43827 Gi02064
Alicyclobacillus acidocaldarius acidocaldarius 104-IA, DSM 446 Bacteria Firmicutes draft 2500575013 29405 DSM 446 Gi02324
Anaerococcus prevotii PC 1, DSM 20548 Bacteria Firmicutes draft 2500645363 29533 DSM 20548 Gi02318
Atopobium parvulum IPP 1246, DSM 20469 Bacteria Actinobacteria draft 2500575011 29401 DSM 20469 Gi02317
Beutenbergia cavernosa HKI 0122, DSM 12333 Bacteria Actinobacteria draft 2500395322 20827 DSM 12333 Gi02225
Brachybacterium faecium DSM 4810 Bacteria Actinobacteria finished 2500153401 17026 DSM 4810 Gi02066
Brachyspira murdochii DSM 12563 Bacteria Spirochaetes draft 2500645365 29543 DSM 12563 Gi02313
Capnocytophaga ochracea DSM 7271 Bacteria Bacteroidetes draft 2500575012 29403 DSM 7271 Gi02305
Catenulispora acidiphila ID139908, DSM 44928 Bacteria Actinobacteria draft 2500395338 21085 DSM 44928 Gi02233
Cellulomonas flavigena 134, DSM 20109 Bacteria Actinobacteria draft 2500395336 19707 DSM 20109 Gi02067
Chitinophaga pinensis UQM 2034, DSM 2588 Bacteria Bacteroidetes draft 2500395347 27951 DSM 2588 Gi02244
Conexibacter woesei ID131577, DSM 14684 Bacteria Actinobacteria draft 2500347307 20745 DSM 14684 Gi02154
Cryptobacterium curtum DSM 15641 Bacteria Actinobacteria finished 2500332002 20739 DSM 15641 Gi02234
Denitrovibrio acetiphilus N2460, DSM 12809 Bacteria Deferribacteres draft 2500575016 29431 DSM 12809 Gi02322
Desulfohalobium retbaense DSM 5692 Bacteria Deltaproteobacteria draft 2500575018 29199 DSM 5692 Gi02246
Desulfomicrobium baculatum DSM 04028 Bacteria Deltaproteobacteria draft 2500645356 29527 DSM 4028 Gi02302
Desulfotomaculum acetoxidans 5575, DSM 771 Bacteria Firmicutes draft 2500395337 27947 DSM 771 Gi02239
Dethiosulfovibrio peptidovorans SEBR 4207, DSM 11002 Bacteria Aminanaerobia draft 2500549401 20741 DSM 11002 Gi02152
Dyadobacter fermentans NS 114, DSM 18053 Bacteria Bacteroidetes draft 2500395342 20829 DSM 18053 Gi02155
Eggerthella lenta VPI 0255, DSM 2243 Bacteria Actinobacteria draft 2500549402 21093 DSM 2243 Gi02242
Geodermatophilus obscurus DSM 43160 Bacteria Actinobacteria draft 2500645366 29547 DSM 43160 Gi02257
Gordonia bronchialis DSM 43247 Bacteria Actinobacteria draft 2500645367 29549 DSM 43247 Gi02258
Haliangium ochraceum SMP-2, DSM 14365 Bacteria Deltaproteobacteria draft 2500395339 28711 DSM 14365 Gi02251
Halogeometricum borinquense DSM 11551 Archaea Halobacteria finished 2500153400 20743 DSM 11551 Gi02153
Halomicrobium mukohataei arg-2, DSM 12286 Archaea Halobacteria draft 2500395343 27945 DSM 12286 Gi02248
Halorhabdus utahensis AX-2, DSM 12940 Archaea Halobacteria draft 2500575004 29305 DSM 12940 Gi02250
Jonesia denitrificans DSM 20603 Bacteria Actinobacteria draft 2500168153 20833 DSM 20603 Gi02227
Kangiella koreensis SW-125, DSM 16069 Bacteria Gammaproteobacteria draft 2500645353 29443 DSM 16069 Gi02314
Kribbella flavida DSM 17836 Bacteria Actinobacteria draft 2500395325 21089 DSM 17836 Gi02235
Kytococcus sedentarius DSM 20547 Bacteria Actinobacteria finished 2500168150 21067 DSM 20547 Gi02226
Leptotrichia buccalis C-1013-b, DSM 1135 Bacteria Fusobacteria draft 2500645352 29445 DSM 1135 Gi02240
Meiothermus ruber DSM 1279 Bacteria Deinococci draft 2500395348 28827 DSM 1279 Gi02300
Meiothermus silvanus DSM 9946 Bacteria Deinococci draft 2500645369 29551 DSM 9946 Gi02308
Nakamurella multipartita DSM 44233 Bacteria Actinobacteria draft 2500645368 21081 DSM 44233 Gi02230
Nocardiopsis dassonvillei dassonvillei DSM 43111 Bacteria Actinobacteria draft 2500395320 19709 DSM 43111 Gi02065
Pedobacter heparinus HIM 762-3, DSM 2366 Bacteria Bacteroidetes draft 2500395321 27949 DSM 2366 Gi02243
Planctomyces limnophilus DSM 3776 Bacteria Bacteroidetes draft 2500575009 29411 DSM 3776 Gi02301
Rhodothermus marinus DSM 4252 Bacteria Bacteroidetes draft 2500575002 29281 DSM 4252 Gi02303
Saccharomonospora viridis P101, DSM 43017 Bacteria Actinobacteria finished 2500347305 20835 DSM 43017 Gi02228
Sanguibacter keddieii DSM 10542 Bacteria Actinobacteria finished 2500153403 19711 DSM 10542 Gi02151
Sebaldella termitidis ATCC 33386 Bacteria Fusobacteria draft 2500645364 29539 ATCC 33386 Gi02490
Slackia heliotrinireducens DSM 20476 Bacteria Actinobacteria finished 2500168151 20831 DSM 20476 Gi02157
Sphaerobacter thermophilus 4ac11, DSM 20745 Bacteria Chloroflexi draft 2500347306 21087 DSM 20745 Gi02236
Spirosoma linguale DSM 74 Bacteria Bacteroidetes draft 2500395346 28817 DSM 74 Gi02298
Stackebrandtia nassauensis LLR-40K-21, DSM 44728 Bacteria Actinobacteria draft 2500549403 19713 DSM 44728 Gi02068
Streptobacillus moniliformis DSM 12112 Bacteria Fusobacteria draft 2500575005 29309 DSM 12112 Gi02312
Streptosporangium roseum NI 9100, DSM 43021 Bacteria Actinobacteria draft 2500395335 21083 DSM 43021 Gi02229
Sulfurospirillum deleyianum DSM 6946 Bacteria Epsilonproteobacteria draft 2500645361 29529 DSM 6946 Gi02323
Thermanaerovibrio acidaminovorans Su883 DSM 6589 Bacteria Aminanaerobia draft 2500645362 29531 DSM 6589 Gi02247
Thermobaculum terrenum YNP1, ATCC BAA-798 Bacteria Chloroflexi draft 2500645355 29523 ATCC BAA-798 Gi02489
Thermobispora bispora DSM 43833 Bacteria Actinobacteria finished 2500194801 20737 DSM 43833 Gi02237
Thermomonospora curvata DSM 43183 Bacteria Actinobacteria draft 2500645351 20825 DSM 43183 Gi02238
Tsukamurella paurometabola DSM 20162 Bacteria Actinobacteria draft 2500575010 29399 DSM 20162 Gi02254
Veillonella parvula Te3, DSM 2008 Bacteria Firmicutes draft 2500347300 21091 DSM 2008 Gi02241
Xylanimonas cellulosilytica DSM 15894 Bacteria Actinobacteria draft 2500153402 19715 DSM 15894 Gi02069
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45. GEBA Pilot V:
Benefit?
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46. Why Increase Taxonomic Coverage?
• Mechanisms of diversification
• Gene discovery
• Annotation, functional prediction
• Metagenomic analysis
• Species phylogeny and classification
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47. Value of 100 diverse genomes I:
Gene discovery
• Gene families
– Will compare and contrast gene family
diversity in these genomes versus random
samples of previous genomes
– Will assess rate of gene family discovery and
whether / how much it is diminishing
• Specific examples of novelty
– Focusing on DOE mission areas
– Do we find novel forms of hydrogenases,
cellulases, C-fixation, etc
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48. Value of 100 diverse genomes II:
Annotation
• Ortholog identification
– Filling in gaps will help identify orthologs between species
– Diverse GC content and amino acid composition should also
improve ortholog identification
• Examination of the rate of hypothetical protein conversion
to “known” proteins
• Non-homology functional prediction should improve
greatly
– Phylogenetic profiling
– Rosetta Stone domain sharing
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49. QuickTime™ and a
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Based on Wu et al. 2005
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50. QuickTime™ and a
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51. Value of 100 diverse genomes III:
Metagenomics
• More diverse genomes should improve anchoring
and binning of all metagenomic data sets
• Will test by running phylotyping software
comparing to genome data sets with and without
GEBA genomes
– Megan
– AMPHORA
• Should be a good complement to reference
genome sequencing
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52. dnaG
0.7
frr
infC
0.6 nusA
pgk
pyrG
0.5 rplA
rplB
rplC
0.4 rplD
rplE
rplF
0.3
rplK
rplL
0.2 rplM
rplN
rplP
0.1 rplS
rplT
rpmA
0 rpoB
rpsB
rpsC
Aquificae Chlorobi rpsE
Chlamydiae Firmicutes
Chloroflexi
Acidobacteria
Bacteroidetes Spirochaetes rpsI
Cyanobacteria Actinobacteria
Planctomycetes rpsJ
Betaproteobacteria
Deltaproteobacteria
Alphaproteobacteria rpsK
Epsilonproteobacteria Unclassified Bacteria
Gammaproteobacteria rpsM
Unclassified Proteobacteria rpsS
smpB
tsf
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53. Value of 100 diverse genomes IV:
Mechanisms of Diversification
• Lateral gene transfer
– Lateral gene transfer is fundamentally important in
microbial evolution
– However, when we find “foreign” DNA in genomes we
usually cannot pinpoint the origin of that DNA
– Having more diverse genomes may help better pin
down source groups for each piece of foreign DNA
• Eukaryotic diversification
– Of ~200 eukaryotic specific gene families
– How many now show up in bacteria and archaea
– Any patterns to where there are found?
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54. CRISPR - expanding the possible
34 out of 56 genomes contain CRISPR
1-13 arrays (loci) per genome
Halingium ochraceum SMP-2, DSM 14365
807 repeats in total
a single repeat contains 382 repeats
Verminephrobacter eisenieae: 249 repeats
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55. Value of 100 diverse genomes V:
Phylogeny
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56. 16s Says Hyphomonas is in Rhodobacteriales
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Badger et al.
2005
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57. WGT Says Its Related to Caulobacterales
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Badger et al.
2005
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58. Tree of Life Example II
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59. QuickTime™ and a
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60. GEBA - What’s Next
• Repeat and/or scale up
• Need to determine the value of finished
versus unfinished genomes
• Apply this method to other groups
– Microbial eukaryotes
– Viruses
• Really fill in bacterial and archaeal tree
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61. The slopes of the linear regression Lines represent the PD contribution of the genomes
(each window contains 50 genomes)
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62. Slope (50 genome windows)
Window position
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63. Greengenes ssrRNA
Slope (50 genome windows)
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64. GEBA: Long Run
• Need active community input
• Involvement of multiple funding agencies,
labs, genome centers
• Integration/ communication among all large
scale projects
• Follow recommendations of NAS, ASM,
AAM reports
• Adopt a Microbe - Link to educational
initiatives
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