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DNA and the hidden world of microbes


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Talk by Jonathan Eisen for CLIMB2011 Symposium at UC Davis.

Published in: Health & Medicine, Technology
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DNA and the hidden world of microbes

  1. DNA & MicrobesDNA and the Hidden World of Microbes CLIMB Symposium September 12, 2011 Jonathan A. Eisen University of California, Davis
  2. Robin in London Examples
  4. Microbes are smallSize* They are small, by definition* Were not really known untilmicroscope invention
  5. But there are LOTS of themNumbers* 100 million in gram of soil* More cells on Earth than starsin universe* More biomass than plants,animals* 10x cells on humans thanhuman cells* 50x10^6 viruses/ml sea water
  6. Diversity I: Form
  7. Diversity II: Function
  8. Function 1: The Bad
  9. Function 2: The Good Nitrogen Fixation Animal NutritionCarbon Fixation
  10. Function 3: The Unknown
  11. Function 4: The UnusualH2S, pH 0, 95°C CO, 80°C High salt low pH CO2 4°C105°CCH3
  12. Function 5: Food, Fuel, etc Feed microbes a little carbon and they can make some nice things
  13. Function 6: Running the Planet Carbon cycle Nitrogen cycle
  14. Studying microbial diversity• Two main questions • Who is out there? • What are they doing?
  15. Sequencing and Microbes• Sequencing is useful as a tool in studies of microbial diversity for many reasons• It is complimentary to other means of study• Four major “ERAs” in use of sequencing for microbial diversity studies
  16. Era I: rRNA Tree of Life
  17. Era I: rRNA Tree of Life Bacteria • Appearance of microbes not informative (enough) • rRNA Tree of Life Archaea identified two major groups of organisms w/o nuclei • rRNA powerful for many reasons, though not perfect EukaryotesBarton, Eisen et al. “Evolution”, CSHL Press. 2007.Based on tree from Pace 1997 Science 276:734-740
  18. Diversity III: Phylogenetic• Three main kinds of organisms • Bacteria • Archaea • Eukaryotes• Viruses not alive, but some call them microbes• Many misclassifications occurred before the use of molecular methods
  19. The Tree of Life 2006adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
  20. The Tree of Life 2006adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
  21. Era II: rRNA in environment
  22. Culturing Microbes
  23. Great Plate Count AnomalyCulturing Microscope Count Count
  24. Great Plate Count AnomalyCulturing Microscope Count <<<< Count
  25. Great Plate Count Anomaly DNACulturing Microscope Count <<<< Count
  26. Culturing Microbes
  27. Culturing Microbes
  28. Plant/Animal Field Studies
  29. Plant/Animal Field Studies
  30. Plant/Animal Field Studies
  31. Plant/Animal Field Studies
  32. Plant/Animal Field Studies
  33. Plant/Animal Field Studies
  34. Plant/Animal Field Studies
  35. Microbial Field Studies
  36. Microbial Field Studies
  37. Microbial Field Studies
  38. Microbial Field Studies
  39. Microbial Field Studies
  40. Microbial Field Studies
  41. Microbial Field Studies
  42. Microbial Field Studies
  43. CSI Microbiology Collect from environment
  44. CSI Microbiology Collect from environment
  45. rRNA PCR DNA extraction PCR Makes lots Sequence PCR of copies of rRNA genes the rRNA genes in sample rRNA1 5’...ACACACATAGGTGGAGC TAGCGATCGATCGA... 3’ Phylogenetic tree Sequence alignment = Data matrix rRNA2 rRNA1 rRNA2 rRNA1 A C A C A C 5’..TACAGTATAGGTGGAGCT rRNA4 AGCGACGATCGA... 3’rRNA3 rRNA2 T A C A G T rRNA3 rRNA3 C A C T G T 5’...ACGGCAAAATAGGTGGA E. coli Humans rRNA4 C A C A G T TTCTAGCGATATAGA... 3’ Yeast E. coli A G A C A G rRNA4 5’...ACGGCCCGATAGGTGG Humans T A T A G T ATTCTAGCGCCATAGA... 3’ Yeast T A C A G T
  46. Comparing Sequences• Analogous to comparing bones
  47. 1992 rRNA PCR and me .... NOTES 3419 A. pisum P A. piswn S Tx. nivea L awaaa sym L equizenata syr L Cud orbgcdar s,ym rs. gesgosterorn - / I -- V I N. gonorrhoeae B. Uhar.opkiuns sym 5% C. magncisca sym Tns. sp. L-12 A. tnefaciens JOURNAL OF BACTERIOLOGY, May 1992, p. 3416-3421 0021-9193/92/103416-06$02.00/0 Vol. 174, No. 10 Copyright © 1992, American Society for Microbiology Phylogenetic Relationships of Chemoautotrophic Bacterial R. ricketsil Symbionts of Solemya velum Say (Mollusca: Bivalvia) Determined by 16S rRNA Gene Sequence Analysis JONATHAN A. EISEN,lt STEVEN W. SMITH,2 AND COLLEEN M. CAVANAUGH`* Department of Organismic and Evolutionary Biology, 1 and Harvard Genome Laboratory,2 Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138 Received 4 November 1991/Accepted 9 March 1992 The protobranch bivalve Solemya velum Say (Mollusca: Bivalvia) houses chemoautotrophic symbionts intracellularly within its gills. These symbionts were characterized through sequencing of polymerase chain rRNA regions and hybridization of an Escherichia coli gene probe to S. velum
  48. Major phyla of bacteria & archaea No cultures Some cultures
  49. The Hidden Majority Richness estimates Hugenholtz 2002 Bohannan and Hughes 2003
  50. CensoredCensored
  51. Era III: Genome Sequencing
  52. 1st Genome Sequence Fleischmann et al. 1995
  53. Genomes Revolutionized Microbiology• Predictions of metabolic processes• Better vaccine and drug design• New insights into mechanisms of evolution• Genomes serve as template for functional studies• New enzymes and materials for engineering and synthetic biology
  54. Metabolic Predictions
  55. Lateral Gene TransferPerna et al. 2003
  56. Network of LifeBacteria Archaea Eukaryotes Figure from Barton, Eisen et al. “Evolution”, CSHL Press. Based on tree from Pace NR, 2003.
  57. Using the Core
  58. WhWhole genome treebuilt usingAMPHORAby Martin Wu andDongying Wu
  59. Microbial genomes From
  60. Phylogenetic Diversity• Phylogenetic diversity poorly sampled• GEBA project at DOE- JGI correcting this
  61. Era IV: Genomes in Environment
  62. Novel Form of Phototrophy Beja et al. 2000
  63. Era IV: Genomes in Environment shotgun sequenceMetagenomics
  64. Metagenomics Challenge
  65. Binning challenge
  66. Weighted % of Clones 0 0.1250 0.2500 0.3750 0.5000 Al ph a Be pro ta teo G p b am rot ac m eo te ba ria Ep ap ct si ro lo t e np eob ria D el rot ac ta e t pr ob eria ot ac C eo te ya b rEFG no ac iaEFTurRNARecARpoB b teHSP70 Fi act ria rm e Ac ic ria tin ut es ob a C cte hl r or ia ob C i FB C hl o Major Phylogenetic Group Sp rof Sargasso Phylotypes iro lex i Fu cha D304: 66. 2004 Metagenomic Phylotyping ei so et no ba es co ct cc er Euus ia ry -T a hVenter et al., Science C rcherm re na aeous rc t ha a eo ta
  67. Metagenomics & Ecology
  68. Field Diversity
  69. Sequencing Technology
  70. Generation I: Manual Sanger
  71. Generation II: Automation
  72. Generation III: No clones
  73. Generation IV: ????
  74. Acknowledgements• $$$ • DOE • NSF • GBMF • Sloan • DARPA• People, places • DOE JGI: Eddy Rubin, Phil Hugenholtz et al. • UC Davis: Aaron Darling, Dongying Wu • Other: Jessica Green, Katie Pollard, Martin Wu, Tom Slezak, Jack Gilbert