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Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project
 

Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project

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    Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project Talk by J. Eisen at ASBMB on "Phylogeny driven genomic encyclopedia" project Presentation Transcript

    • A Phylogeny-Driven Genomic Encyclopedia of Bacteria and Archaea Jonathan A. Eisen Talk for ASBMB April 25, 2010 Sunday, April 25, 2010
    • Eisen Lab - Phylogenomics of Novelty Origin of New Genome Functions and Dynamics Processes •Evolvability •New genes •Repair and •Changes in old genes recombination processes •Changes in pathways •Intragenomic variation Species Evolution •Phylogenetic history •Vertical vs. horizontal descent •Needed to track gain/loss of processes, infer convergence Sunday, April 25, 2010
    • Bacterial evolve Sunday, April 25, 2010
    • TIGR Fleischmann et al. 1995 Sunday, April 25, 2010
    • Microbial genomes From http://genomesonline.org Sunday, April 25, 2010
    • Sunday, April 25, 2010
    • rRNA Tree of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
    • The Tree is not Happy Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
    • 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 Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
    • Proteobacteria 2002 TM6 OS-K Acidobacteria • At least 40 Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
    • Proteobacteria 2002 TM6 OS-K Acidobacteria • At least 40 Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some other Verrucomicrobia Chlamydia OP3 phyla are Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 Thermomicrobia sampled Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
    • Proteobacteria 2002 TM6 OS-K Acidobacteria • At least 40 Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some other Verrucomicrobia Chlamydia OP3 phyla are Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 Thermomicrobia sampled Chloroflexi TM7 Deinococcus-Thermus • Same trend in Dictyoglomus Aquificae Thermudesulfobacteria Archaea Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
    • Proteobacteria 2002 TM6 OS-K Acidobacteria • At least 40 Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Genome WS3 Gemmimonas Firmicutes sequences are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some other Verrucomicrobia Chlamydia OP3 phyla are Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 Thermomicrobia sampled Chloroflexi TM7 Deinococcus-Thermus • Same trend in Dictyoglomus Aquificae Thermudesulfobacteria Eukaryotes Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
    • Filling in the Genomic Phylogenetic Gaps • Common approach within some eukaryotic groups • Many small projects funded to fill in some bacterial or archaeal gaps • Phylogenetic gaps in bacterial and archaeal projects commonly lamented in literature Sunday, April 25, 2010
    • Proteobacteria • NSF-funded TM6 OS-K • At least 40 Tree of Life Acidobacteria Termite Group phyla of OP8 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 Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some other Verrucomicrobia Chlamydia OP3 phyla are only Planctomycetes Spriochaetes sparsely Coprothmermobacter OP10 Thermomicrobia sampled Chloroflexi TM7 Deinococcus-Thermus • Solution I: Dictyoglomus Aquificae sequence more Eisen & Ward, PIs Thermudesulfobacteria Thermotogae OP1 phyla OP11 Sunday, April 25, 2010
    • The Tree of Life is Still Angry Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
    • Major Lineages of Actinobacteria 2.5 Actinobacteria 2.5.1 Acidimicrobidae 2.5.1 Acidimicrobidae 2.5.1.1 Unclassified 2.5.1.2 "Microthrixineae 2.5.1.1 Unclassified 2.5.1.3 Acidimicrobineae 2.5.1.3.1 Unclassified 2.5.1.2 "Microthrixineae 2.5.1.3.2 Acidimicrobiaceae 2.5.1.4 BD2-10 2.5.1.3 Acidimicrobineae 2.5.1.5 EB1017 2.5.2 Actinobacteridae 2.5.1.4 BD2-10 2.5.2.1 Unclassified 2.5.2.10 Ellin306/WR160 2.5.1.5 EB1017 2.5.2.11 Ellin5012 2.5.2.12 Ellin5034 2.5.2 Actinobacteridae 2.5.2.13 Frankineae 2.5.2.13.1 Unclassified 2.5.2.1 Unclassified 2.5.2.13.2 Acidothermaceae 2.5.2.10 Ellin306/WR160 2.5.2.13.3 2.5.2.13.4 Ellin6090 Frankiaceae 2.5.2.11 Ellin5012 2.5.2.13.5 2.5.2.13.6 Geodermatophilaceae Microsphaeraceae 2.5.2.12 Ellin5034 2.5.2.13.7 2.5.2.14 Sporichthyaceae Glycomyces 2.5.2.13 Frankineae 2.5.2.15 2.5.2.15.1 Intrasporangiaceae Unclassified 2.5.2.14 Glycomyces 2.5.2.15.2 2.5.2.15.3 Dermacoccus Intrasporangiaceae 2.5.2.15 Intrasporangiaceae 2.5.2.16 2.5.2.17 Kineosporiaceae Microbacteriaceae 2.5.2.16 Kineosporiaceae 2.5.2.17.1 2.5.2.17.2 Unclassified Agrococcus 2.5.2.17 Microbacteriaceae 2.5.2.17.3 2.5.2.18 Agromyces Micrococcaceae 2.5.2.18 Micrococcaceae 2.5.2.19 2.5.2.2 Micromonosporaceae Actinomyces 2.5.2.19 Micromonosporaceae 2.5.2.20 2.5.2.20.1 Propionibacterineae Unclassified 2.5.2.2 Actinomyces 2.5.2.20.2 2.5.2.20.3 Kribbella Nocardioidaceae 2.5.2.20 Propionibacterineae 2.5.2.20.4 2.5.2.21 Propionibacteriaceae Pseudonocardiaceae 2.5.2.21 Pseudonocardiaceae 2.5.2.22 2.5.2.22.1 Streptomycineae Unclassified 2.5.2.22 Streptomycineae 2.5.2.22.2 2.5.2.22.3 Kitasatospora Streptacidiphilus 2.5.2.23 Streptosporangineae 2.5.2.23 2.5.2.23.1 Streptosporangineae Unclassified 2.5.2.3 Actinomycineae 2.5.2.23.2 2.5.2.23.3 Ellin5129 Nocardiopsaceae 2.5.2.4 Actinosynnemataceae 2.5.2.23.4 2.5.2.23.5 Streptosporangiaceae Thermomonosporaceae 2.5.2.5 Bifidobacteriaceae 2.5.2.3 Actinomycineae 2.5.2.4 Actinosynnemataceae 2.5.2.6 Brevibacteriaceae 2.5.2.5 Bifidobacteriaceae 2.5.2.6 Brevibacteriaceae 2.5.2.7 Cellulomonadaceae 2.5.2.7 Cellulomonadaceae 2.5.2.8 Corynebacterineae 2.5.2.8 Corynebacterineae 2.5.2.8.1 Unclassified 2.5.2.8.2 Corynebacteriaceae 2.5.2.9 Dermabacteraceae 2.5.2.8.3 Dietziaceae 2.5.2.8.4 Gordoniaceae 2.5.3 Coriobacteridae 2.5.2.8.5 Mycobacteriaceae 2.5.2.8.6 Rhodococcus 2.5.3.1 Unclassified 2.5.2.8.7 Rhodococcus 2.5.2.8.8 Rhodococcus 2.5.3.2 Atopobiales 2.5.2.9 Dermabacteraceae 2.5.2.9.1 Unclassified 2.5.3.3 Coriobacteriales 2.5.2.9.2 Brachybacterium 2.5.2.9.3 Dermabacter 2.5.3.4 Eggerthellales 2.5.3 Coriobacteridae 2.5.3.1 Unclassified 2.5.4 OPB41 2.5.3.2 Atopobiales 2.5.3.3 Coriobacteriales 2.5.5 PK1 2.5.3.4 Eggerthellales 2.5.4 OPB41 2.5.6 Rubrobacteridae 2.5.5 PK1 2.5.6 Rubrobacteridae 2.5.6.1 Unclassified 2.5.6.1 Unclassified 2.5.6.2 "Thermoleiphilaceae 2.5.6.2 "Thermoleiphilaceae 2.5.6.2.1 Unclassified 2.5.6.2.2 Conexibacter 2.5.6.3 MC47 2.5.6.2.3 XGE514 2.5.6.3 MC47 2.5.6.4 Rubrobacteraceae 2.5.6.4 Rubrobacteraceae Sunday, April 25, 2010
    • Microbial genomes 2010- ... From http://genomesonline.org Sunday, April 25, 2010
    • Proteobacteria TM6 OS-K • At least 100 phyla of Acidobacteria Termite Group OP8 bacteria Nitrospira Bacteroides Chlorobi • Genome sequences are 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 Chloroflexi • Solution - use tree to really TM7 Deinococcus-Thermus fill gaps Dictyoglomus Aquificae Well sampled phyla Thermudesulfobacteria Thermotogae OP1 OP11 Sunday, April 25, 2010
    • Why Increase Phylogenetic Coverage? • Gene discovery • Annotation, functional prediction • Metagenomic analysis • Mechanisms of diversification • Species phylogeny and classification Sunday, April 25, 2010
    • A Genomic Encyclopedia of Bacteria and Archaea (GEBA) Sunday, April 25, 2010
    • GEBA Pilot Project Overview • Identify major branches in rRNA tree for which no genomes are available • Identify a cultured representative for each group • Grow > 200 of these and prep. DNA • Sequence and finish 100 • Annotate, analyze, release data • Assess benefits of tree guided sequencing • Paper published in Nature Dec. 2009. Sunday, April 25, 2010
    • B: Ac tin ob ac te B: ria # of Genomes Am (H Sunday, April 25, 2010 in igh 10 15 20 25 30 35 0 5 an G a C B: B: er ) Ba Aq ob ct uif ia e i B: B: ro cae D Ch ide B: efe lo te r s D rri ofl ef ba e B: e c xi B: De B rrib ter Ep lta : D act es si Pr ei er lo o n es n te oc Pr ob oc ot a ci B: e ct G B: oba eri am B F ct a : ir e B: m Fu mi ria a G P so cut em ro ba e t c s B: ma eo te ba ri H tim c a a t B: loa ona eri a B: Pl nae de an r te Th c o s Phyla er B: to bia m S m le y s B: od piro ce es c te T u h B: he lfo ae s rm b te GEBA Pilot Target List Th o a s er de cte m s ri u a A: ove lfo H n bi A: alo abu a A: A b la M rc ac e A: et ha te M han eo ria et g ha ob lob ac i A: no te m r A: The icr ia Th rm obi er oc a m oc op ci ro te i
    • GEBA and Openness • All data being released as quickly as possible with no restrictions to IMG-GEBA; Genbank, etc • Data also available in Biotorrents (http://biotorrents.net) • Individual genome reports being published in new Open Access journal “Standards in Genome Sciences (SIGS)” • Main GEBA paper in Nature freely available and published using Creative Commons License Sunday, April 25, 2010
    • Assess Benefits of GEBA • All genomes have some value • But what, if any, is the benefit of tree- guided sequencing over other selection methods • Lessons for other large scale microbial genome projects? Sunday, April 25, 2010
    • GEBA Lesson 1 rRNA Tree is Useful for Identifying Phylogenetically Novel Genomes rRNA Tree topology is not perfect; Genome-based trees better Sunday, April 25, 2010
    • rRNA Tree of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
    • Sunday, April 25, 2010
    • Network of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
    • Wh Whole genome tree built using AMPHORA by Martin Wu and Dongying Wu Sunday, April 25, 2010
    • PD of rRNA, Genome Trees Similar From Wu et al. 2009 Sunday, April 25, 2010
    • Proteobacteria Sunday, April 25, 2010
    • GEBA Lesson 2 Phylogenetically-guided genome selection improves genome annotation Sunday, April 25, 2010
    • Predicting Function • Key step in genome projects • More accurate predictions help guide experimental and computational analyses • Many diverse approaches • Comparative and evolutionary analysis greatly improves most predictions Sunday, April 25, 2010
    • Most/All Functional Prediction Improves w/ Better Phylogenetic Sampling • Better definition of protein family sequence “patterns” • Conversion of hypothetical into conserved hypotheticals • Greatly improves “comparative” and “evolutionary” based predictions • Linking distantly related members of protein families • Improved non-homology prediction Sunday, April 25, 2010
    • From Wu et al. 2009. Sunday, April 25, 2010
    • GEBA Lesson 3 Improves analysis of genome data from uncultured organisms Sunday, April 25, 2010
    • Metagenomics shotgun clone Sunday, April 25, 2010
    • Sunday, April 25, 2010
    • rRNA phylotyping from metagenomics Venter et al., 2004 Sunday, April 25, 2010
    • Shotgun Sequencing Allows Use of Alternative Anchors (e.g., RecA) Venter et al., 2004 Sunday, April 25, 2010
    • Weighted % of Clones 0 0.1250 0.2500 0.3750 0.5000 Al ph ap ro t eo Be b ac ta pr t er ot e ia G Sunday, April 25, 2010 am ob ac m t er ap ia ro Ep te si ob lo ac np t er ro ia De t eo lta b ac pr te ot ria eo b C ac ya t er n ob ia ac t er Fi ia rm ic u te Ac s tin ob ac ter C ia hl or ob i C FB Major Phylogenetic Group Sargasso Phylotypes C hl or of le Sp xi iro c ha et Fu es so De ba in ct er oc ia oc cu s- Eu The ry r ar mu ch s ae C ot re a na rc ha eo ta Shotgun Sequencing Allows Use of Other Markers Venter et al., 2004 EFG EFTu rRNA RecA RpoB HSP70
    • Weighted % of Clones 0 0.1250 0.2500 0.3750 0.5000 Al ph ap ro t eo Be b ac ta pr t er ot e ia G Sunday, April 25, 2010 am ob ac m t er ap ia ro Ep te si ob lo ac np t er ro ia De t eo lta b ac pr te ot ria eo b C ac ya t er n ob ia ac t er Fi ia rm ic u te Ac s tin ob ac ter C ia hl or ob i without good C FB Major Phylogenetic Group Sargasso Phylotypes C Cannot be done hl or of le Sp xi iro c ha et Fu es so De ba in ct er oc ia sampling of genomes oc cu s- Eu The ry r ar mu ch s ae C ot re a na rc ha eo ta Shotgun Sequencing Allows Use of Other Markers Venter et al., 2004 EFG EFTu rRNA RecA RpoB HSP70
    • Binning challenge A T B U C V D W E X F Y G Z Sunday, April 25, 2010
    • Binning challenge A T B U C V D W E X F Y G Best binning method: reference genomes Z Sunday, April 25, 2010
    • Binning challenge A T B U C V D W E X F Y G No reference genome? What do you do? Z Sunday, April 25, 2010
    • Binning challenge A T B U C V D W E X F Y G No reference genome? What do you do? Z Phylogeny .... Sunday, April 25, 2010
    • Al ph ap ro Be te ta o ba G p 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 am ro ct te er m o ia Sunday, April 25, 2010 ap ba ro ct D t er el eo ia ta ba Ep pr ct ot er U si lo eo ia nc ba la np ct ss ro er ifi te ia ed ob Pr ac ot te eo ria ba Cy ct an er ob ia ac Ch te ria la m Ac yd id ia ob e Ba ac te ct ria er Ac oi de tin te ob s ac te ria Aq Pl ui an fic ct om ae yc Sp et AMPHORA - each read on its own tree iro es ch ae Fi te rm s ic ut Ch es lo ro U fle nc xi la Ch ss lo ifi ro ed bi Ba ct er ia Phylogenetic Binning Using AMPHORA frr tsf pgk rplL rplF rplP rplT rplE infC rpsI rplS rplA rplB rplK rplC rpsJ rplN rplD rplM rpsE rpsS rpsB rpsK rpsC rpoB rpsM pyrG nusA dnaG rpmA smpB
    • Phylogenetic Binning Using AMPHORA dnaG 0.7 frr infC 0.6 nusA pgk pyrG 0.5 0.4 Cannot be done rplA rplB rplC rplD 0.3 without good rplE rplF rplK rplL 0.2 0.1 sampling of genomes rplM rplN rplP rplS rplT rpmA 0 rpoB rpsB es ia s es s ria ia ia bi ia ia om ae e ia ria ria ria xi te te ia er er er er er er fle ro et ut rpsC fic te te te te yd de ae ct ct ct ct ct ct lo yc ro ic ac ac ac ac ui m ch oi ba ba Ch ba ba ba Ba rm rpsE lo Aq ob ob ob ob er la iro eo Ch o eo o eo Fi ed Ch ct an te te te id tin ct rpsI Sp ot ot t Ba Ac ro ro ro ro ifi an Cy Ac Pr pr ss ap p ap np rpsJ Pl ta ta ed la ph m lo el Be nc rpsK si ifi am Al D Ep U ss rpsM G la nc rpsS U smpB tsf AMPHORA - each read on its own tree Sunday, April 25, 2010
    • GEBA Phylogenomic Lesson 5 We have still only scratched the surface of microbial diversity Sunday, April 25, 2010
    • Protein Family Rarefaction Curves • Take data set of multiple complete genomes • Identify all protein families using MCL • Plot # of genomes vs. # of protein families Sunday, April 25, 2010
    • Sunday, April 25, 2010
    • Sunday, April 25, 2010
    • Sunday, April 25, 2010
    • Sunday, April 25, 2010
    • Sunday, April 25, 2010
    • Mobile Motility Element? Sunday, April 25, 2010
    • Phylogenetic Distribution Novelty: Bacterial Actin Related Protein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aliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam Zemla, Victor Kunin See also Guljamow et al. 2007 Current Biology. Sunday, April 25, 2010
    • rRNA Tree of Life Bacteria Archaea Eukaryotes FIgure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003. Sunday, April 25, 2010
    • Phylogenetic Diversity: Sequenced Bacteria & Archaea From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html Sunday, April 25, 2010
    • Phylogenetic Diversity with GEBA From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html Sunday, April 25, 2010
    • Phylogenetic Diversity: Isolates From Wu et al. 2009. Sunday, April 25, 2010
    • Phylogenetic Diversity: All From Wu et al. 2009. http://www.nature.com/nature/journal/v462/n7276/full/nature08656.html Sunday, April 25, 2010
    • Proteobacteria TM6 OS-K • At least 40 phyla of Acidobacteria Termite Group OP8 bacteria Nitrospira Bacteroides Chlorobi • Genome sequences are 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 Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Well sampled phyla Thermudesulfobacteria Thermotogae Poorly sampled OP1 OP11 No cultured taxa Sunday, April 25, 2010
    • Uncultured Lineages: Technical Approaches • Get into culture • Enrichment cultures • If abundant in low diversity ecosystems • Flow sorting • Microbeads • Microfluidic sorting • Single cell amplification Sunday, April 25, 2010
    • GEBA Phylogenomic Lesson 6 Need Experiments from Across the Tree of Life too Sunday, April 25, 2010
    • 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 OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
    • As of 2002 Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Experimental WS3 Gemmimonas Firmicutes studies are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
    • As of 2002 Proteobacteria TM6 OS-K • At least 40 Acidobacteria Termite Group OP8 phyla of Nitrospira Bacteroides bacteria Chlorobi Fibrobacteres Marine GroupA • Experimental WS3 Gemmimonas Firmicutes studies are Fusobacteria Actinobacteria mostly from OP9 Cyanobacteria Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some studies Verrucomicrobia Chlamydia OP3 in other phyla Planctomycetes Spriochaetes Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Thermudesulfobacteria Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
    • 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 Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some other Verrucomicrobia Chlamydia OP3 phyla are Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 Thermomicrobia sampled Chloroflexi TM7 Deinococcus-Thermus • Same trend in Dictyoglomus Aquificae Thermudesulfobacteria Eukaryotes Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
    • 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 Synergistes three phyla Deferribacteres Chrysiogenetes NKB19 • Some other Verrucomicrobia Chlamydia OP3 phyla are Planctomycetes Spriochaetes only sparsely Coprothmermobacter OP10 Thermomicrobia sampled Chloroflexi TM7 Deinococcus-Thermus • Same trend in Dictyoglomus Aquificae Thermudesulfobacteria Viruses Thermotogae OP1 Based on OP11 Hugenholtz, 2002 Sunday, April 25, 2010
    • Proteobacteria TM6 OS-K Need Acidobacteria Termite Group OP8 experimental Nitrospira Bacteroides Chlorobi studies from Fibrobacteres Marine GroupA WS3 across the tree Gemmimonas Firmicutes too Fusobacteria Actinobacteria OP9 Cyanobacteria Synergistes Deferribacteres Chrysiogenetes NKB19 Verrucomicrobia Chlamydia OP3 Planctomycetes Spriochaetes 0.1 Coprothmermobacter OP10 Thermomicrobia Chloroflexi TM7 Deinococcus-Thermus Dictyoglomus Aquificae Tree based on Thermudesulfobacteria Thermotogae Hugenholtz (2002) OP1 with some OP11 modifications. Sunday, April 25, 2010
    • Sunday, April 25, 2010
    • MICROBES Sunday, April 25, 2010
    • A Happy Tree of Life Sunday, April 25, 2010
    • GEBA Pilot Project: Components • Project overview (Phil Hugenholtz, Nikos Kyrpides, Jonathan Eisen, Eddy Rubin, Jim Bristow) • Project management (David Bruce, Eileen Dalin, Lynne Goodwin) • Culture collection and DNA prep (DSMZ, Hans-Peter Klenk) • Sequencing and closure (Eileen Dalin, Susan Lucas, Alla Lapidus, Mat Nolan, Alex Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng) • Annotation and data release (Nikos Kyrpides, Victor Markowitz, et al) • Analysis (Dongying Wu, Kostas Mavrommatis, Martin Wu, Victor Kunin, Neil Rawlings, Ian Paulsen, Patrick Chain, Patrik D’Haeseleer, Sean Hooper, Iain Anderson, Amrita Pati, Natalia N. Ivanova, Athanasios Lykidis, Adam Zemla) • Adopt a microbe education project (Cheryl Kerfeld) • Outreach (David Gilbert) • $$$ (DOE, Eddy Rubin, Jim Bristow) Sunday, April 25, 2010