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A phylogeny driven genomic 
encyclopedia of bacteria and 
archaea 
Jonathan A. Eisen 
UC Davis 
! 
Culture Collection Meet...
http:// 
www.google. 
com/ 
http:// 
www.google.c 
om/imgres? 
https:// 
www.google.c 
om/url? 
http://www.microbe.net/
http:// 
www.google. 
com/ 
http:// 
www.google.c 
om/imgres? 
https:// 
www.google.c 
om/url?
GEBA
As of 2002
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Saving Sequenced Strains 
• Of 266 genomes done or in progress in 2011 
• 138 were type strain for their species 
• 32 did...
Saving Sequenced Strains 
We propose that the following standards should be 
adopted by the entire community. First, genom...
Saving Sequenced Strains 
Recommended Policy: 
! 
Order strains for sequencing from Culture Collections to 
guarantee one ...
Organisms Selected 
Phylum 
Species selected 
Chrysiogenes 
Chrysiogenes arsenatis (GCA) 
Coprothermobacter 
Coprothermoba...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Major Lineages of Actinobacteria 
2.5.1 Acidimicrobidae 
2.5.1.1 Unclassified 
2.5.1.2 "Microthrixineae 
2.5.1.3 Acidimicr...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
• At least 40 phyla 
of bacteria 
• Genome 
sequences are 
mostly from three 
phyla 
• Some other phyla 
are only sparsely...
Filling in the Tree 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Filling in the Tree 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Filling in the Tree 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Filling in the Tree 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Lots of Plants, Animals, Fungi 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
Exclude Plants, Animals, Fungi 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
A Genomic Encyclopedia of Microbes (GEM) 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al ...
Just Say No to Eukaryotes 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
GEBA: A Genomic Encyclopedia 
of Bacteria and Archaea 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on B...
GEBA
GEBA Pilot Project: Components 
• Project overview (Phil Hugenholtz, Nikos Kyrpides, Jonathan 
Eisen, Eddy Rubin, Jim Bris...
Lesson 1: rRNA PD IDs novel lineages 
From Wu et al. 2009 Nature 462, 1056-1060
Lesson 2: rRNA Tree is not perfect 
16s WGT, 23S 
Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.
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 “...
Lesson 9: Improves metagenomics 
Sargasso Phylotypes 
Weighted % of Clones 
0.500 
0.375 
0.250 
0.125 
0.000 
GEBA Projec...
Lesson 4 : Metadata & Data Papers
Lesson 5: Project management critical 
• Tracking samples and status 
• Getting permissions 
• Shipping samples 
• Contact...
Lesson 6: Culture Collections Needed
GEBA Biggest Challenge: 
Getting DNA 
• Getting quality DNA is biggest bottleneck 
• Solution: Beg Borrow and Steal 
! 
• ...
Quantification gel of the genomic DNA isolated from Microorganisms 
Conexibacter woesei (DSM 14684T) 
1 2 3 4 5 6 7 8 
Lan...
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 Halo...
49 
Plan: 
Sequence multiple Root Nodule Bacteria (RNBs) across the 
planet. Pilot: 100 RNBs. 
Beta RNB 
Cupriavidis 
Burk...
Future?
Future 1: Massive Diversity 
From Wu et al. 2009 Nature 462, 1056-1060
JGI Dark Matter Project 
TG HSM SM G ETL 
AK E 
environmental 
samples (n=9) 
isolation of single 
cells (n=9,600) 
BS E 
...
Future 2: Eukaryotes and Viruses 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
A Genomic Encyclopedia of Microbes (GEM) 
Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al ...
Future 3 
• Need Experiments from Across the Tree 
of Life too
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fibrobacteres 
Marine Gro...
Need 
experimental 
studies from 
across the tree 
too 
0.1 
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 ...
Adopt a 
Microbe 
0.1 
Proteobacteria 
TM6 
OS-K 
Acidobacteria 
Termite Group 
OP8 
Nitrospira 
Bacteroides 
Chlorobi 
Fi...
http:// 
www.google. 
com/ 
http:// 
www.google.c 
om/imgres? 
https:// 
www.google.c 
om/url? 
http://www.microbe.net/
The Genomic Encyclopedia of Bacteria and Archaea & the Need for A Built Environment Culture Collection
The Genomic Encyclopedia of Bacteria and Archaea & the Need for A Built Environment Culture Collection
The Genomic Encyclopedia of Bacteria and Archaea & the Need for A Built Environment Culture Collection
The Genomic Encyclopedia of Bacteria and Archaea & the Need for A Built Environment Culture Collection
The Genomic Encyclopedia of Bacteria and Archaea & the Need for A Built Environment Culture Collection
The Genomic Encyclopedia of Bacteria and Archaea & the Need for A Built Environment Culture Collection
The Genomic Encyclopedia of Bacteria and Archaea & the Need for A Built Environment Culture Collection
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The Genomic Encyclopedia of Bacteria and Archaea & the Need for A Built Environment Culture Collection

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

  1. 1. A phylogeny driven genomic encyclopedia of bacteria and archaea Jonathan A. Eisen UC Davis ! Culture Collection Meeting September 24, 2014
  2. 2. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? http://www.microbe.net/
  3. 3. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url?
  4. 4. GEBA
  5. 5. As of 2002
  6. 6. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • At least 40 phyla of bacteria As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  7. 7. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  8. 8. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  9. 9. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  10. 10. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  11. 11. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • 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, Robb, Nelson, et al Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  12. 12. 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.
  13. 13. Saving Sequenced Strains We 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.
  14. 14. Saving Sequenced Strains Recommended 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.
  15. 15. Organisms Selected Phylum Species selected Chrysiogenes Chrysiogenes arsenatis (GCA) Coprothermobacter Coprothermobacter proteolyticus (GCBP) Dictyoglomi Dictyoglomus thermophilum (GDT) Thermodesulfobacteria Thermodesulfobacterium commune (GTC) Nitrospirae Thermodesulfovibrio yellowstonii (GTY) Thermomicrobia Thermomicrobium roseum (GTR ) Deferribacteres Geovibrio thiophilus (GGT) Synergistes Synergistes jonesii (GSJ)
  16. 16. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 OP1 OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Still highly biased in terms of the tree • NSF-funded Tree of Life Project • A genome from each of eight phyla Eisen & Ward, PIs Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  17. 17. 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 2.5.6.3 MC47 2.5.6.4 Rubrobacteraceae 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 2.5.6.2.3 XGE514 2.5.6.3 MC47 2.5.6.4 Rubrobacteraceae
  18. 18. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 OP1 OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Same trend in Archaea • NSF-funded Tree of Life Project • A genome from each of eight phyla Eisen & Ward, PIs Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  19. 19. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 OP1 OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Same trend in Eukaryotes • NSF-funded Tree of Life Project • A genome from each of eight phyla Eisen & Ward, PIs Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  20. 20. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 OP1 OP11 • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Same trend in Viruses • NSF-funded Tree of Life Project • A genome from each of eight phyla Eisen & Ward, PIs Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  21. 21. • At least 40 phyla of bacteria • Genome sequences are mostly from three phyla • Some other phyla are only sparsely sampled • Solution: Really Fill in the Trees Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 OP1 OP11 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  22. 22. Filling in the Tree Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  23. 23. Filling in the Tree Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  24. 24. Filling in the Tree Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  25. 25. Filling in the Tree Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  26. 26. Lots of Plants, Animals, Fungi Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  27. 27. Exclude Plants, Animals, Fungi Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  28. 28. A Genomic Encyclopedia of Microbes (GEM) Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  29. 29. Just Say No to Eukaryotes Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  30. 30. GEBA: A Genomic Encyclopedia of Bacteria and Archaea Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  31. 31. GEBA
  32. 32. 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)
  33. 33. Lesson 1: rRNA PD IDs novel lineages From Wu et al. 2009 Nature 462, 1056-1060
  34. 34. Lesson 2: rRNA Tree is not perfect 16s WGT, 23S Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.
  35. 35. Lesson 3: Improves Analysis Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.
  36. 36. Synapomorphies exist
  37. 37. 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
  38. 38. Lesson 9: Improves metagenomics Sargasso Phylotypes Weighted % of Clones 0.500 0.375 0.250 0.125 0.000 GEBA Project improves metagenomic analysis Firmicutes Actinobacteria Major Phylogenetic Group Betaproteobacteria Gammaproteobacteria Alphaproteobacteria Deltaproteobacteria Epsilonproteobacteria Cyanobacteria Chlorobi CFB Chloroflexi Fusobacteria Deinococcus-Thermus Spirochaetes Euryarchaeota Crenarchaeota EFG EFTu HSP70 RecA RpoB rRNA Venter et al., Science 304: 66-74. 2004
  39. 39. Lesson 4 : Metadata & Data Papers
  40. 40. 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
  41. 41. Lesson 6: Culture Collections Needed
  42. 42. 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
  43. 43. Quantification gel of the genomic DNA isolated from Microorganisms Conexibacter woesei (DSM 14684T) 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 9 10 11 12 13 14 15 16 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 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).
  44. 44. GEBA Cyanobacteria www.pnas.org/cgi/doi/10.1073/pnas.1217107110
  45. 45. 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
  46. 46. 49 Plan: Sequence multiple Root Nodule Bacteria (RNBs) across the planet. Pilot: 100 RNBs. Beta RNB Cupriavidis Burkholderia Alpha RNB Azorhizobium Allorhizobium Bradyrhizobium Mesorhizobium Rhizobium Sinorhizobium Devosia Ochrobactrum Phyllobacterium Balneimonas-like 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 $US 6-10 billion annually on N fertilizer. • Grain and animal production enhanced by fixed nitrogen supplied by the symbiosis. Nikos Kyrpides GEBA RNB
  47. 47. Future?
  48. 48. Future 1: Massive Diversity From Wu et al. 2009 Nature 462, 1056-1060
  49. 49. JGI Dark Matter Project TG HSM SM G ETL AK E environmental samples (n=9) isolation of single cells (n=9,600) BS E whole genome amplification (n=3,300) SSU rRNA gene based identification (n=2,000) genome sequencing, assembly and QC (n=201) draft genomes (n=201) SAK HOT OT GOM GBS EPR TA PR OM seawater brackish/freshwater hydrothermal sediment bioreactor Korarchaeota Cren Thermoprotei Thaumarchaeota Cren MCG Cren pISA7 Cren C2 Aigarchaeota Nanoarchaea Micrarchaea DSEG (Aenigmarchaea) Nanohaloarchaea pMC2A384 (Diapherotrites) Euryarchaeota (*1 OP11 (Microgenomates) OD1 (Parcubacteria) SR1 BH1 TM7 GN02 (Gracilibacteria) Bacteriodetes OP1 (Acetothermia) F58>@,@,,AB&CG56?AB =D)&'E C=1 ZB3 4896@9/,-565B TG3 Spirochaetes WWE1 (Cloacamonetes) Proteobacteria 486?8,A-5B Tenericutes 4AB@9/,-568/ Chrysiogenetes Chlorobi *;<%0123=/68>8?8,6@98/: Caldithrix GOUTA4 Acidobacteria Elusimicrobia Nitrospirae 49S1 2B Chloroflexi Caldiserica AD3 OP9 (Atribacteria) ()*&2 Synergistetes Thermodesulfobacteria Deferribacteres CD12 (Aerophobetes) OP8 (Aminicenantes) AC1 SBR1093 SPAM GAL15 Dictyoglomi EM3 Thermotogae Aquificae GAL35 EM19 (Calescamantes) +,-*./'&'012345678#89/,-568/: Deltaproteobacteria Cyanobacteria ()*&2 Actinobacteria Gemmatimonadetes NC10 SC4 WS2 NKB19 (Hydrogenedentes) WYO Armatimonadetes WS4 Planctomycetes Chlamydiae OP3 (Omnitrophica) Lentisphaerae Verrucomicrobia BRC1 Poribacteria WS1 !"#$%&'$ LD1 GN01 WS3 (Latescibacteria) GN04 BACTERIA ARCHAEA HGT from Eukaryotes (Nanoarchaea) oxidoretucase Ribo ADP + ' Ribo ' e- donor + O + e- acceptor sigma factor (Diapherotrites, Nanoarchaea) !4 "#$#"% !2 !3 !1 -35 -10 stringent response (Diapherotrites, Nanoarchaea) SpotT RelA ppGpp limiting amino acids (GTP or GDP) archaeal toxins (Nanoarchaea) lytic murein transglycosylase + PPi GTP or GDP +ATP limiting phosphate, fatty acids, carbon, iron DksA Expression of components for stress response &'() &*() +',#-./0123452 H '62 Reduction Oxidation H ADP '6 O H 2 ',)+## $ # 6 #+# $ # 7 2 -# ####################',)6 Eukaryota UGA recoded for Gly (Gracilibacteria) A A * U archaeal type purine synthesis PRPP ;,<*,+ ' ' H O '62 ' 68*62 OH (Microgenomates) PurF PurD 9:3' PurL/Q PurM PurK PurE 9:3* PurB H O '6 *8*63 6#2#' O + 68*62 O '6 *8*63 tetra-peptide O O ' 68*62 OH PurP O '6 *8*63 O 68*62 O '6 *8*63 tetra-peptide murein (peptido-glycan) Archaea ? adenine guanine ' ' H H ' H ' H IMP ,<*,+ * A * U G G U G U A * G U A U A * U Growing AA chain =+',>?/0@# recognizes UGA 1+', ribosome Woyke et al. Nature 2013.
  50. 50. Future 2: Eukaryotes and Viruses Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  51. 51. A Genomic Encyclopedia of Microbes (GEM) Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
  52. 52. Future 3 • Need Experiments from Across the Tree of Life too
  53. 53. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • At least 40 phyla of bacteria As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  54. 54. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • At least 40 phyla of bacteria • Experimental studies are mostly from three phyla As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  55. 55. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • At least 40 phyla of bacteria • Experimental studies are mostly from three phyla • Some studies in other phyla As of 2002 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  56. 56. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • 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 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  57. 57. Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 • 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 Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  58. 58. Need experimental studies from across the tree too 0.1 Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 Tree based on Hugenholtz (2002) with some modifications. Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  59. 59. Adopt a Microbe 0.1 Proteobacteria TM6 OS-K Acidobacteria Termite Group OP8 Nitrospira Bacteroides 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 Aquificae Dictyoglomus Thermudesulfobacteria Thermotogae OP1 OP11 Tree based on Hugenholtz (2002) with some modifications. Tree Based on Hugenholtz, 2002. http://genomebiology.com/ 2002/3/2/reviews/0003
  60. 60. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? http://www.microbe.net/

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