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. A phylogeny driven genomic encyclopedia of bacteria and archaea Jonathan A. Eisen UC Davis ! Culture Collection Meeting September 24, 2014
- 2. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? http://www.microbe.net/
- 3. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url?
- 4. GEBA
- 5. As of 2002
- 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. 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. 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. 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. 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. 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. 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. 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. 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. 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)
- 17. 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
- 18. 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
- 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 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
- 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 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
- 21. 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
- 22. • 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
- 23. Filling in the Tree Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 24. Filling in the Tree Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 25. Filling in the Tree Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 26. Filling in the Tree Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 27. Lots of Plants, Animals, Fungi Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 28. Exclude Plants, Animals, Fungi Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 29. A Genomic Encyclopedia of Microbes (GEM) Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 30. Just Say No to Eukaryotes Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 31. GEBA: A Genomic Encyclopedia of Bacteria and Archaea Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 32. GEBA
- 33. 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)
- 34. Lesson 1: rRNA PD IDs novel lineages From Wu et al. 2009 Nature 462, 1056-1060
- 35. Lesson 2: rRNA Tree is not perfect 16s WGT, 23S Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.
- 36. Lesson 3: Improves Analysis Badger et al. 2005 Int J System Evol Microbiol 55: 1021-1026.
- 43. 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
- 44. 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
- 45. Lesson 4 : Metadata & Data Papers
- 46. 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
- 47. Lesson 6: Culture Collections Needed
- 48. 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
- 50. 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).
- 52. 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
- 53. 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 $US 6-10 billion annually on N fertilizer. • Grain and animal production enhanced by fixed nitrogen supplied by the symbiosis. Nikos Kyrpides GEBA RNB
- 54. Future?
- 55. Future 1: Massive Diversity From Wu et al. 2009 Nature 462, 1056-1060
- 56. JGI Dark Matter Project TG HSM SM G ETL AK E environmental samples (n=9) isolation of single cells (n=9,600) BS E whole genome amplification (n=3,300) SSU rRNA gene based identification (n=2,000) genome sequencing, assembly and QC (n=201) draft genomes (n=201) SAK HOT OT GOM GBS EPR TA PR OM seawater brackish/freshwater hydrothermal sediment bioreactor Korarchaeota Cren Thermoprotei Thaumarchaeota Cren MCG Cren pISA7 Cren C2 Aigarchaeota Nanoarchaea Micrarchaea DSEG (Aenigmarchaea) Nanohaloarchaea pMC2A384 (Diapherotrites) Euryarchaeota (*1 OP11 (Microgenomates) OD1 (Parcubacteria) SR1 BH1 TM7 GN02 (Gracilibacteria) Bacteriodetes OP1 (Acetothermia) F58>@,@,,AB&CG56?AB =D)&'E C=1 ZB3 4896@9/,-565B TG3 Spirochaetes WWE1 (Cloacamonetes) Proteobacteria 486?8,A-5B Tenericutes 4AB@9/,-568/ Chrysiogenetes Chlorobi *;<%0123=/68>8?8,6@98/: Caldithrix GOUTA4 Acidobacteria Elusimicrobia Nitrospirae 49S1 2B Chloroflexi Caldiserica AD3 OP9 (Atribacteria) ()*&2 Synergistetes Thermodesulfobacteria Deferribacteres CD12 (Aerophobetes) OP8 (Aminicenantes) AC1 SBR1093 SPAM GAL15 Dictyoglomi EM3 Thermotogae Aquificae GAL35 EM19 (Calescamantes) +,-*./'&'012345678#89/,-568/: Deltaproteobacteria Cyanobacteria ()*&2 Actinobacteria Gemmatimonadetes NC10 SC4 WS2 NKB19 (Hydrogenedentes) WYO Armatimonadetes WS4 Planctomycetes Chlamydiae OP3 (Omnitrophica) Lentisphaerae Verrucomicrobia BRC1 Poribacteria WS1 !"#$%&'$ 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.
- 57. Future 2: Eukaryotes and Viruses Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 58. A Genomic Encyclopedia of Microbes (GEM) Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 59. Future 3 • Need Experiments from Across the Tree of Life too
- 60. 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
- 61. 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
- 62. 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
- 63. 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
- 64. 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
- 65. 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
- 66. 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
- 67. http:// www.google. com/ http:// www.google.c om/imgres? https:// www.google.c om/url? http://www.microbe.net/