1.The Importance of History (and other obsessions)Jonathan A. EisenUC DavisTalk for Lake Arrowhead MicrobialGenomes 2010 (#LAMG10) Wednesday, September 15, 2010

2. Wednesday, September 15, 2010 3. Social Networking in Science Wednesday, September 15, 2010 4. Bacterial evolve Wednesday, September 15, 2010 5. Evolution of Lake Arrowhead Wednesday, September 15, 2010 6. Blast Peptide LAKEARROWHEAD Wednesday, September 15, 2010 7. Wednesday, September 15, 2010 8. Wednesday, September 15, 2010 9. Wednesday, September 15, 2010 10. Homework Do blastp search with other famous people associated with Lake Arrowhead Meeting JEFFREYHMILLER SARAHPALIN and her relationship to fungi B. fuckeliana see http://phylogenomics.blogspot.com/ 2008/09/tracing-evolutionary-history-of- sarah.htmlWednesday, September 15, 2010 11. 2010Wednesday, September 15, 2010 12. 2008Wednesday, September 15, 2010 13. 2006Wednesday, September 15, 2010 14. 2004Wednesday, September 15, 2010 15. No 2002 Wednesday, September 15, 2010 16. Wayback Machine Wednesday, September 15, 2010 17. 2002Wednesday, September 15, 2010 18. Wednesday, September 15, 2010 19. Quotes 2004 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 lightWednesday, September 15, 2010 20. Wednesday, September 15, 2010 21. Quotes 2006 The human guts are a real milieu of stuff You better kiss everybody Microbes not only have a lot of sex, they have a lot of weird sex This is how you do metagenomics on 50 dollars, and thats Canadian dollars Wednesday, September 15, 2010 22. Quotes 2008 Antibiotics do not kill things, they corrupt them There comes a point in life when you have to bringchemists into the picture The rectal swabs are here in tan color And there's Jeffrey Dahmer We are the environment. We live the phenotype. If I have time I will tell you about a dream A paper came out next year Wednesday, September 15, 2010 23. Quotes 2010 We have been using this word for many years without actually realizing itwas correct Another thing you need to know" pause "Actually you don't NEED toknow any of this "I have been inuenced by Fisher Price throughout my life Don't take that away from us It takes 1000 nanobiologists to make one microbiologist I am going to wrap up as I hear the crickets chirping And we will bring out the unused cheese from yesterday In an engineering sense, the vagina is a simple plug ow reactor This is going to be ironic coming from someone who studies circumcision A little bit about time, but I am going to spend a lot less time on time thanon space Wednesday, September 15, 2010 24. Keywords I remember from 2010 Penis Vagina Anthrax Acne Ulcer (multiple kinds) Global warming Antibiotic resistance Virulence 24Wednesday, September 15, 2010 25. Wednesday, September 15, 2010 26. Wednesday, September 15, 2010 27. rRNA Tree of Life Bacteria ArchaeaEukaryotes FIgure from Barton, Eisen et al. Evolution, CSHL Press. Based on tree from Pace NR, 2003. Wednesday, September 15, 2010 28. Proteobacteria 2002 TM6 OS-K Acidobacteria At least 40 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 Chloroexi TM7 Deinococcus-Thermus Dictyoglomus Aquicae Thermudesulfobacteria Thermotogae OP1 Based on Hugenholtz, OP112002 Wednesday, September 15, 2010 29. 2002 Proteobacteria TM6 OS-K At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA Genome WS3 Gemmimonassequences are Firmicutes Fusobacteriamostly from Actinobacteria OP9 Cyanobacteria three phyla Synergistes Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroexi TM7 Deinococcus-Thermus Dictyoglomus Aquicae Thermudesulfobacteria Thermotogae OP1 Based on Hugenholtz, OP112002 Wednesday, September 15, 2010 30. 2002 Proteobacteria TM6 OS-K At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA Genome WS3 Gemmimonassequences are Firmicutes Fusobacteriamostly from Actinobacteria OP9 Cyanobacteria three phyla Synergistes Deferribacteres Chrysiogenetes Some other NKB19 Verrucomicrobia Chlamydia phyla are only OP3 Planctomycetes Spriochaetes sparsely Coprothmermobacter OP10 sampled Thermomicrobia Chloroexi TM7 Deinococcus-Thermus Dictyoglomus Aquicae Thermudesulfobacteria Thermotogae OP1 Based on Hugenholtz, OP112002 Wednesday, September 15, 2010 31. 2002 Proteobacteria TM6 OS-K At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA Genome WS3 Gemmimonassequences are Firmicutes Fusobacteriamostly from Actinobacteria OP9 Cyanobacteria three phyla Synergistes Deferribacteres Chrysiogenetes Some other NKB19 Verrucomicrobia Chlamydia phyla are only OP3 Planctomycetes Spriochaetes sparsely Coprothmermobacter OP10 sampled Thermomicrobia Chloroexi TM7 Deinococcus-Thermus Dictyoglomus Aquicae Thermudesulfobacteria Thermotogae OP1 Based on Hugenholtz, OP112002 Wednesday, September 15, 2010 32. Why Increase Phylogenetic Coverage? Common approach within some eukaryotic groups (FGP, NHGRI, etc) Many successful small projects to ll in bacterial or archaeal gaps Phylogenetic gaps in bacterial and archaeal projects commonly lamented in literature Many potential benets Wednesday, September 15, 2010 33. Proteobacteria NSF-fundedTM6 At least 40 phyla OS-K Tree of LifeAcidobacteria Termite Group of bacteria OP8 Project Nitrospira Genome Bacteroides Chlorobi A genomeFibrobacteres Marine GroupA sequences are from each ofWS3 Gemmimonasmostly from eight phyla Firmicutes Fusobacteriathree phyla Actinobacteria OP9 Cyanobacteria Synergistes Some other Deferribacteres Chrysiogenetesphyla are only NKB19 Verrucomicrobia Chlamydia sparsely sampled OP3 Planctomycetes Spriochaetes Solution I: Coprothmermobacter OP10sequence more Thermomicrobia Chloroexi TM7 phyla Deinococcus-Thermus Dictyoglomus AquicaeEisen & Ward, PIsThermudesulfobacteria Thermotogae OP1 OP11Wednesday, September 15, 2010 34. Wednesday, September 15, 2010 35. Proteobacteria NSF-fundedTM6 At least 40 phyla OS-K Tree of LifeAcidobacteria Termite Group of bacteria OP8 Project Nitrospira Genome Bacteroides Chlorobi A genomeFibrobacteres Marine GroupA sequences are from each ofWS3 Gemmimonasmostly from eight phyla Firmicutes Fusobacteriathree phyla Actinobacteria OP9 Cyanobacteria Synergistes Some other Deferribacteres Chrysiogenetesphyla are only NKB19 Verrucomicrobia Chlamydia sparsely sampled OP3 Planctomycetes Spriochaetes Still highly Coprothmermobacter OP10biased in terms Thermomicrobia Chloroexi TM7 of the tree Deinococcus-Thermus Dictyoglomus AquicaeEisen & Ward, PIsThermudesulfobacteria Thermotogae OP1 OP11Wednesday, September 15, 2010 36. Major Lineages of Actinobacteria 2.5 Actinobacteria2.5.1Acidimicrobidae 2.5.1Acidimicrobidae 2.5.1.1Unclassified2.5.1.2"Microthrixineae 2.5.1.1Unclassified2.5.1.3Acidimicrobineae2.5.1.3.1Unclassified 2.5.1.2"Microthrixineae2.5.1.3.2Acidimicrobiaceae2.5.1.4BD2-10 2.5.1.3Acidimicrobineae2.5.1.5EB10172.5.2Actinobacteridae 2.5.1.4BD2-102.5.2.1Unclassified2.5.2.10 Ellin306/WR160 2.5.1.5EB10172.5.2.11 Ellin50122.5.2.12 Ellin5034 2.5.2Actinobacteridae2.5.2.13 Frankineae2.5.2.13.1 Unclassified 2.5.2.1Unclassified2.5.2.13.2 Acidothermaceae2.5.2.13.3 Ellin6090 2.5.2.10 Ellin306/WR1602.5.2.13.4 Frankiaceae2.5.2.11 Ellin5012 2.5.2.13.52.5.2.13.6 Geodermatophilaceae Microsphaeraceae2.5.2.12 Ellin5034 2.5.2.13.72.5.2.14 Sporichthyaceae Glycomyces2.5.2.13 Frankineae2.5.2.152.5.2.15.1 Intrasporangiaceae Unclassified 2.5.2.14 Glycomyces2.5.2.15.22.5.2.15.3 Dermacoccus Intrasporangiaceae 2.5.2.15 Intrasporangiaceae2.5.2.162.5.2.17 Kineosporiaceae Microbacteriaceae 2.5.2.16 Kineosporiaceae 2.5.2.17.12.5.2.17.2 Unclassified Agrococcus 2.5.2.17 Microbacteriaceae 2.5.2.17.32.5.2.18 Agromyces Micrococcaceae 2.5.2.18 Micrococcaceae2.5.2.192.5.2.2 Micromonosporaceae Actinomyces 2.5.2.19 Micromonosporaceae2.5.2.202.5.2.20.1 Propionibacterineae Unclassified 2.5.2.2Actinomyces 2.5.2.20.22.5.2.20.3 Kribbella Nocardioidaceae 2.5.2.20 Propionibacterineae 2.5.2.20.42.5.2.21 Propionibacteriaceae Pseudonocardiaceae 2.5.2.21 Pseudonocardiaceae2.5.2.222.5.2.22.1 Streptomycineae Unclassified 2.5.2.22 Streptomycineae 2.5.2.22.22.5.2.22.3 Kitasatospora Streptacidiphilus 2.5.2.23 Streptosporangineae 2.5.2.232.5.2.23.1 Streptosporangineae Unclassified 2.5.2.3Actinomycineae2.5.2.23.22.5.2.23.3 Ellin5129 Nocardiopsaceae 2.5.2.4Actinosynnemataceae 2.5.2.23.42.5.2.23.5 Streptosporangiaceae Thermomonosporaceae 2.5.2.5Bifidobacteriaceae2.5.2.32.5.2.4 Actinomycineae Actinosynnemataceae 2.5.2.6Brevibacteriaceae 2.5.2.5Bifidobacteriaceae2.5.2.6Brevibacteriaceae 2.5.2.7Cellulomonadaceae 2.5.2.7Cellulomonadaceae2.5.2.8Corynebacterineae 2.5.2.8Corynebacterineae 2.5.2.8.1Unclassified2.5.2.8.2Corynebacteriaceae 2.5.2.9Dermabacteraceae2.5.2.8.3Dietziaceae2.5.2.8.4Gordoniaceae 2.5.3Coriobacteridae 2.5.2.8.5Mycobacteriaceae2.5.2.8.6Rhodococcus 2.5.3.1Unclassified2.5.2.8.7Rhodococcus2.5.2.8.8Rhodococcus 2.5.3.2Atopobiales 2.5.2.9Dermabacteraceae2.5.2.9.1Unclassified 2.5.3.3Coriobacteriales2.5.2.9.2Brachybacterium2.5.2.9.3Dermabacter 2.5.3.4Eggerthellales2.5.3Coriobacteridae2.5.3.1Unclassified 2.5.4OPB41 2.5.3.2Atopobiales2.5.3.3Coriobacteriales 2.5.5PK1 2.5.3.4Eggerthellales2.5.4OPB41 2.5.6Rubrobacteridae 2.5.5PK12.5.6Rubrobacteridae 2.5.6.1Unclassified2.5.6.1Unclassified2.5.6.2"Thermoleiphilaceae 2.5.6.2"Thermoleiphilaceae 2.5.6.2.1Unclassified2.5.6.2.2Conexibacter 2.5.6.3MC472.5.6.2.3XGE5142.5.6.3MC47 2.5.6.4Rubrobacteraceae2.5.6.4Rubrobacteraceae Wednesday, September 15, 2010 37. Proteobacteria NSF-fundedTM6 At least 40 phyla OS-K Tree of LifeAcidobacteria Termite Group of bacteria OP8 Project Nitrospira Genome Bacteroides Chlorobi A genomeFibrobacteres Marine GroupA sequences are from each ofWS3 Gemmimonasmostly from eight phyla Firmicutes Fusobacteriathree phyla Actinobacteria OP9 Cyanobacteria Synergistes Some other Deferribacteres Chrysiogenetesphyla are only NKB19 Verrucomicrobia Chlamydia sparsely sampled OP3 Planctomycetes Spriochaetes Same trend in Coprothmermobacter OP10Archaea Thermomicrobia Chloroexi TM7 Deinococcus-Thermus Dictyoglomus AquicaeEisen & Ward, PIsThermudesulfobacteria Thermotogae OP1 OP11Wednesday, September 15, 2010 38. Proteobacteria NSF-fundedTM6 At least 40 phyla OS-K Tree of LifeAcidobacteria Termite Group of bacteria OP8 Project Nitrospira Genome Bacteroides Chlorobi A genomeFibrobacteres Marine GroupA sequences are from each ofWS3 Gemmimonasmostly from eight phyla Firmicutes Fusobacteriathree phyla Actinobacteria OP9 Cyanobacteria Synergistes Some other Deferribacteres Chrysiogenetesphyla are only NKB19 Verrucomicrobia Chlamydia sparsely sampled OP3 Planctomycetes Spriochaetes Same trend in Coprothmermobacter OP10Eukaryotes Thermomicrobia Chloroexi TM7 Deinococcus-Thermus Dictyoglomus AquicaeEisen & Ward, PIsThermudesulfobacteria Thermotogae OP1 OP11Wednesday, September 15, 2010 39. Proteobacteria NSF-fundedTM6 At least 40 phyla OS-K Tree of LifeAcidobacteria Termite Group of bacteria OP8 Project Nitrospira Genome Bacteroides Chlorobi A genomeFibrobacteres Marine GroupA sequences are from each ofWS3 Gemmimonasmostly from eight phyla Firmicutes Fusobacteriathree phyla Actinobacteria OP9 Cyanobacteria Synergistes Some other Deferribacteres Chrysiogenetesphyla are only NKB19 Verrucomicrobia Chlamydia sparsely sampled OP3 Planctomycetes Spriochaetes Same trend in Coprothmermobacter OP10Viruses Thermomicrobia Chloroexi TM7 Deinococcus-Thermus Dictyoglomus AquicaeEisen & Ward, PIsThermudesulfobacteria Thermotogae OP1 OP11Wednesday, September 15, 2010 40. Proteobacteria GEBATM6 OS-K At least 40 phyla Acidobacteria A genomic Termite Group OP8 of bacteria encyclopediaNitrospira Bacteroides Genome Chlorobi of bacteria and Fibrobacteres Marine GroupA sequences are archaea WS3 Gemmimonasmostly from Firmicutes Fusobacteria Actinobacteria three phyla OP9 Cyanobacteria Synergistes Some other Deferribacteres Chrysiogenetesphyla are only NKB19 Verrucomicrobia Chlamydia sparsely sampled OP3 Planctomycetes Spriochaetes Solution: Really Coprothmermobacter OP10 Thermomicrobia Fill in the Tree Chloroexi TM7 Deinococcus-Thermus Dictyoglomus AquicaeEisen & Ward, PIsThermudesulfobacteria Thermotogae OP1 OP11Wednesday, September 15, 2010 41. GEBA Pilot Project Overview Identify major branches in rRNA tree for which no genomes are available Identify those with a cultured representative in DSMZ DSMZ grew > 200 of these and prepped DNA Sequence and nish 100+ (covering breadth of bacterial/archaea diversity) Annotate, analyze, release data Assess benets of tree guided sequencing 1st paper Wu et al in Nature Dec 2009 Wednesday, September 15, 2010 42. GEBA Pilot Project: Components Project overview (Phil Hugenholtz, Nikos Kyrpides, Jonathan Eisen, Eddy Rubin, Jim Bristow, Tanya Woyke) 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 DHaeseleer, Sean Hooper, Iain Anderson, Amrita Pati, Natalia N. Ivanova, Athanasios Lykidis, Adam Zemla) Adopt a microbe education project (Cheryl Kerfeld) Outreach (David Gilbert) $$$ (DOE, DSMZ, GBMF) Wednesday, September 15, 2010 43. GEBA and Openness All data released as quickly as possible w/ no restrictions to IMG-GEBA; Genbank, etc Data also available in Biotorrents (http:// biotorrents.net) Individual genome reports published in OA Standards in Genome Sciences (SIGS) 1st GEBA paper in Nature freely available and published using Creative Commons License 43Wednesday, September 15, 2010 44. GEBA Lesson 1 rRNA Tree is Useful for IdentifyingPhylogenetically Novel Organisms 44Wednesday, September 15, 2010 45. rRNA Tree of Life Bacteria ArchaeaEukaryotes FIgure from Barton, Eisen et al. Evolution, CSHL Press. Based on tree from Pace NR, 2003. Wednesday, September 15, 2010 46. Network of Life? Bacteria ArchaeaEukaryotes Figure from Barton, Eisen et al. Evolution, CSHL Press. Based on tree from Pace NR, 2003. Wednesday, September 15, 2010 47. Compare PD in rRNA and WGT Wednesday, September 15, 2010 48. PD of rRNA, Genome Trees SimilarFrom Wu et al. 2009 Nature 462, 1056-1060 Wednesday, September 15, 2010 49. GEBA Lesson 2Phylogeny-driven genome selection helps discover new genetic diversity Wednesday, September 15, 2010 50. Network of Life? Bacteria ArchaeaEukaryotes FIgure from Barton, Eisen et al. Evolution, CSHL Press. Based on tree from Pace NR, 2003. Wednesday, September 15, 2010 51. Protein Family Rarefaction Curves Take data set of multiple complete genomes Identify all protein families using MCL Plot # of genomes vs. # of protein families Wednesday, September 15, 2010 52. Wednesday, September 15, 2010 53. Wednesday, September 15, 2010 54. Wednesday, September 15, 2010 55. Wednesday, September 15, 2010 56. Wednesday, September 15, 2010 57. Synapomorphies exist Wednesday, September 15, 2010 58. Phylogenetic Distribution Novelty: Bacterial Actin Related Protein2"#3)&4&*&& !"#*)$*),+%5"#$-.-6&0&1- !"#$%,$-%)( 7"#0(1.8-9& !"#$''+-+,',! 5"#:1,)*&$/0 !"#&$,%+)+-+ !"#$% !"#$%&'()*&& !"#$%&'(%() ((+"#,-.(/01 !"#*+,**'+(;"#01,&-*0 !"#%*+$--(