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"The Quest for A field Guide to the Microbes" talk by Jonathan Eisen February 2, 2014.


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Talk by Jonathan Eisen at "Science in the River City" meeting of Sacramento Area science teachers.

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"The Quest for A field Guide to the Microbes" talk by Jonathan Eisen February 2, 2014.

  1. 1. ! ! The Quest for a Field Guide to the Microbes ! Jonathan A. Eisen @phylogenomics University of California, Davis ! Talk for Science in the River City January 28, 2014
  2. 2. The Quest for A Field Guide to the Microbes Part I: ! My Obsessions
  3. 3. Open Science
  4. 4. X Open Science
  5. 5. Social Media & Science
  6. 6. X Social Media & Science
  7. 7. RedSox • RedSox
  8. 8. X RedSox • RedSox
  9. 9. Microbial Evolution
  10. 10. Microbial Evolution
  11. 11. photo by J. Eisen
  12. 12. The Quest for A Field Guide to the Microbes Part II: ! The Story of a Bird
  13. 13. !13
  14. 14. !13
  15. 15. !14 from
  16. 16. photo by J. Eisen
  17. 17. photo by J. Eisen
  18. 18. photo by J. Eisen
  19. 19. photo by J. Eisen
  20. 20. photo by J. Eisen
  21. 21. photo by J. Eisen
  22. 22. !21 from Google Maps
  23. 23. !22 from Google Maps
  24. 24. !23 from Google Maps
  25. 25. !24 from Google Maps
  26. 26. !25 from Google Maps
  27. 27. !26 from Google Maps
  28. 28. !27 from Google Maps
  29. 29. !28 from Google Maps
  30. 30. photo by J. Eisen
  31. 31. !30
  32. 32. !31 from Google Maps w/ some addition
  33. 33. Robin in London Examples
  34. 34. Field Guides • What should be included • • • • • Catalog of types of organism Functional diversity Biogeography (space and time) Niche information Means for identification • Provides a guide to interpret normal states and abnormalities
  35. 35. MICROBES
  36. 36. ??? ??? ??? MICROBES
  37. 37. The Quest for A Field Guide to the Microbes Part III: ! A Micro Bit 
 about Microbes
  38. 38. The Microbe Challenge • Microbes are small • But diversity and numbers are very high • Appearance not a good indicator of type or function • Field observations of limited value
  39. 39. Diversity of Form
  40. 40. Diversity of Function
  41. 41. Diversity of Function The Bad
  42. 42. Diversity of Function The Bad The Good
  43. 43. Diversity of Function The Bad The Good The Unusual
  44. 44. Diversity of Function The Bad The Consumable The Good The Unusual
  45. 45. Diversity of Function The Bad The Consumable The Good The Burnable The Unusual
  46. 46. Diversity of Function The Bad The Consumable The Good The Burnable The Unusual The Planet
  47. 47. The Quest for A Field Guide to the Microbes Part IV: 
 CSI Microbiology
  48. 48. Plant/Animal Field Studies
  49. 49. Plant/Animal Field Studies
  50. 50. Plant/Animal Field Studies
  51. 51. Plant/Animal Field Studies
  52. 52. Plant/Animal Field Studies
  53. 53. Plant/Animal Field Studies
  54. 54. Plant/Animal Field Studies
  55. 55. Microbial Field Studies
  56. 56. Microbial Field Studies
  57. 57. Microbial Field Studies
  58. 58. Microbial Field Studies
  59. 59. Microbial Field Studies
  60. 60. Microbial Field Studies
  61. 61. Microbial Field Studies
  62. 62. Microbial Field Studies
  63. 63. Culturing Microbes
  64. 64. The GPA
  65. 65. Great Plate Count Anomaly
  66. 66. Great Plate Count Anomaly
  67. 67. Great Plate Count Anomaly Culturing Microscopy
  68. 68. Great Plate Count Anomaly Culturing Count Microscopy Count
  69. 69. Great Plate Count Anomaly Culturing Count Microscopy <<<< Count
  70. 70. Culturing Microbes
  71. 71. Culturing Microbes
  72. 72. Great Plate Count Anomaly Solution??? Culturing Count Microscopy <<<< Count
  73. 73. Great Plate Count Anomaly DNA Culturing Count Microscopy <<<< Count
  74. 74. DNA Use Case I: Who is Out There?
  75. 75. Who is Out There? DNA extraction PCR Makes lots of copies of the rRNA genes in sample PCR Phylogenetic tree rRNA1 Sequence alignment = Data matrix Yeast C A C A C T A C A G T E. coli Humans A Yeast E. coli rRNA1 A G A C A G Humans T A T A G T Sequence rRNA genes rRNA1 5’ ...TACAGTATAGGTG GAGCTAGCGATCGAT CGA... 3’
  76. 76. Mammal Tree
  77. 77. Sequences vs. Bones Carl Woese
  78. 78. The Tree of Life
 2006 adapted from Baldauf, et al., in Assembling the Tree of Life, 2004 !60
  79. 79. The Tree of Life
 2006 adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
  80. 80. Who is Out There? DNA extraction PCR Makes lots of copies of the rRNA genes in sample PCR Phylogenetic tree rRNA1 Sequence alignment = Data matrix rRNA2 Yeast C A C A T A C A G T A G A C A G Humans T A T A G T Yeast T A C A G T rRNA1 5’ ...ACACACATAGGTG GAGCTAGCGATCGAT CGA... 3’ C E. coli Humans A rRNA2 E. coli rRNA1 Sequence rRNA genes rRNA2 5’ ...TACAGTATAGGTG GAGCTAGCGATCGAT CGA... 3’
  81. 81. Who is Out There? DNA extraction PCR Makes lots of copies of the rRNA genes in sample PCR rRNA1 5’...ACACACATAGGTGGAGCTAG CGATCGATCGA... 3’ Phylogenetic tree rRNA1 Sequence alignment = Data matrix rRNA2 rRNA1 Humans E. coli Yeast A C A C A C rRNA2 T A C A G C A C T G T rRNA4 C A C A G T E. coli A G A C A G Humans T A T A G T Yeast T A C A G T rRNA2 5’..TACAGTATAGGTGGAGCTAGC GACGATCGA... 3’ T rRNA3 rRNA4 rRNA3 Sequence rRNA genes rRNA3 5’...ACGGCAAAATAGGTGGATTC TAGCGATATAGA... 3’ rRNA4 5’...ACGGCCCGATAGGTGGATTC TAGCGCCATAGA... 3’
  82. 82. DNA Sequencing Has Gone Crazy 1977 2010 Sanger sequencing method by F. Sanger (PNAS ,1977, 74: 560-564) 1983 1953 2000 1990 1980 Approaching to NGS AAATCGCTAGCGC CGGCGAGCTAGC CGAGCGATCGAGC CGAGCATCGAGTA PCR by K. Mullis (Cold Spring Harb Symp Quant Biol. 1986;51 Pt 1:263-73) Discovery of DNA structure (Cold Spring Harb. Symp. Quant. Biol. 1953;18:123-31) Human Genome Project (Nature , 2001, 409: 860–92; Science, 2001, 291: 1304–1351) 1993 Development of pyrosequencing (Anal. Biochem., 1993, 208: 171-175; Science ,1998, 281: 363-365) Single molecule emulsion PCR 1998 Founded Solexa 1998 Founded 454 Life Science 2000 454 GS20 sequencer (First NGS sequencer) 2005 Solexa Genome Analyzer (First short-read NGS sequencer) Illumina acquires Solexa (Illumina enters the NGS business) 2006 2006 ABI SOLiD (Short-read sequencer based upon ligation) Roche acquires 454 Life Sciences (Roche enters the NGS business) 2007 2007 GS FLX sequencer (NGS with 400-500 bp read lenght) NGS Human Genome sequencing (First Human Genome sequencing based upon NGS technology) 2008 2008 Hi-Seq2000 (200Gbp per Flow Cell) From Slideshare presentation of Cosentino Cristian 2010 Miseq Roche Jr Ion Torrent PacBio Oxford
  83. 83. A Thumb Drive DNA Sequencer? From Oxford Nanopores Web Site
  84. 84. DNA Use II: What Are They Doing?
  85. 85. DNA Use Case III: Forensics
  86. 86. DNA Use Case IV: Human Microbiome
  87. 87. The Human Microbiome
  88. 88. Microbes Can Make Mice Fat Turnbaugh et al Nature. 2006 444(7122):1027-31.
  89. 89. Who Are We?
  90. 90. The Human Microbiome Censored Censored
  91. 91. The Human Microbiome Hair External nose Naris (L) Lat. pinna (R) Lat. pinna (L) Ext. auditory canal (L) Axilla (R) Dorsal tongue Oral cavity Axilla (L) Volar forearm (R) Palm (R) Palm (L) Volar forearm (L) Palmar index finger (R) Gut Umbilicus Palmar index finger (L) Popliteal fossa (R) Plantar foot (R) Plantar foot (L) Popliteal fossa (L) Acinetobacter Actinomycetales Actinomycineae Alistipes Anaerococcus Bacteroidales Bacteroides Bifidobacteriales Branhamella Campylobacter Capnocytophaga Carnobacteriaceae1 Carnobacteriaceae2 Clostridiales Coriobacterineae Corynebacterineae Faecalibacterium Finegoldia Fusobacterium Gemella Lachnospiraceae Lachnospiraceae (inc. sed.) Lactobacillus Leptotrichia Micrococcineae Neisseria Oribacterium Parabacteroides Pasteurella Pasteurellaceae Peptoniphilus Prevotella Prevotellaceae Propionibacterineae Ruminococcaceae Staphylococcus Streptococcus Veillonella Other Naris (R) Forehead Ext. auditory canal (R) Glans penis Labia minora
  92. 92. Variation May Affect Health • Microbial community different in many disease states compared to healthy individuals • Unclear if this is cause or effect in most cases
  93. 93. Colonization Gone Wrong Necrotizing enterocolitis C-sections
  94. 94. Fecal Transplants
  95. 95. DNA Use Case V: Communities
  96. 96. Biogeography
  97. 97. The Built Environment Microbial Biogeography of Public Restroom Surfaces Gilberto E. Flores1, Scott T. Bates1, Dan Knights2, Christian L. Lauber1, Jesse Stombaugh3, Rob Knight3,4, Noah Fierer1,5* Bacteria of Public Restrooms 1 Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado, United States of America, 2 Department of Computer Science, University of Colorado, Boulder, Colorado, United States of America, 3 Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America, 4 Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado, United States of America, 5 Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America Abstract We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, the diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited by bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing of The ISME Journal (2012), 1–11 the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla: & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with hands. On illustrations of the relative abundance of discriminating suggesting fecal contamination of these surfaces. Floor Figure 3. Cartoon toilet surfaces, gut-associated taxa were more prevalent, taxa on public restroom surfaces. Light blue indicates low surfaces dark blue indicates high abundance of taxa. (A) contained several taxa taxa (Propionibacteriaceae, Corynebacteriaceae, abundance while were the most diverse of all communities and Although skin-associated commonly found in soils. Skin-associated Staphylococcaceae especially the Propionibacteriaceae, on all surfaces, they were relatively more abundant on surfaces routinely touched with bacteria, and Streptococcaceae) were abundant dominated surfaces routinely touched with our hands. Certain taxa were more hands. (B) Gut-associated taxa (Clostridiales, Clostridiales group XI, vagina-associated Lactobacillaceae were widelyBacteroidaceae)in female common in female than in male restrooms as Ruminococcaceae, Lachnospiraceae, Prevotellaceae and distributed were most abundant on toilet surfaces. from urine contamination. Use of the SourceTracker algorithm confirmed Nocardioidaceae) taxonomic restrooms, likely (C) Although soil-associated taxa (Rhodobacteraceae, Rhizobiales, Microbacteriaceae and many of our were in low abundance on all restroom surfaces, they were relatively more abundant on the floor of the surfaces. Overall, theseFigure not drawn to scale. observations as human skin was the primary source of bacteria on restroom restrooms we surveyed. results demonstrate that doi:10.1371/journal.pone.0028132.g003 restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear Bacteria linkages between communities on or in different body sites and those communities found on restroom surfaces. More of P show that SourceTracker analysis support the taxonomic the stallgenerally,were likely dispersed manuallypublicwomen used as we Results of human-associated microbes are commonly found in), they this work is relevant to the after health field 1 1 1,2 1,2 1,2 Steven W Kembel , Evan Jones , Jeff Kline , Dale Northcutt , Jason Stenson , on Coupling these observations with those of the patterns highlighted above, indicating that human skin was the the toilet. restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching 1 Bohannan1, G Z Brown1,2 and Jessica L Green1,3 Ann time, the M Womack , Brendan JM 100 of surfaces. SOURCES source of bacteria on all public restroom surfaces bacteria indicate that routine can 1 Bathroomdistribution of gut-associatedon indoor surfaces, an approach of high-throughput analyses ofpathogen communities to determine biogeography.Furthermore, we demonstrate that we use use primary be used to track bacterial transmission and test the By Biology and the Built Environment Center, Institute of Ecology and Evolution, Department of sources the bacteria of urine- and fecal-associated bacteria of dispersal whichexamined, while the human gut was an important source on or could toilets results in Soil un to take swabbing throughout surfaces in While these results are not unexpected, different the restroom. practices. Biology, University of Oregon, Eugene, OR, USA; 2Energy Studies in Buildings Laboratory, efficacy of hygiene around the toilet, and urine was an important source in women’s Water 80 of outside Department of Architecture, University of Oregon, Eugene, OR, USA and 3Santa Fe Institute, public restrooms,highlight the importance of hand-hygiene when using restrooms (Figure 4, Table S4). Contrary to expectations (see they do researchers Mouth Santa Fe, NM, USA om plants Microbial Biogeography of Public by the SourceTracker 6(11): e28132. public microbes vary in ST, surfaces could also be potential restrooms GE, Bates determined thatCitation: Floressince these Knights D, Lauber CL, Stombaugh J, et al. (2011)above), soil was not identifiedRestroom Surfaces. PLoS ONEalgorithm as Urine doi:10.1371/journal.pone.0028132 60 being a major source of bacteria on any of the surfaces, including ours after where theyvehicles from dependcome for the transmission of human pathogens. Unfortunately, Gut Editor: Mark R. Liles, Auburn University, college students floors (Figure 4). Although the floor samples contained family-level previous studies have documented that United States of America are ing on the surface (chart).frequent users of the studied restrooms)(who not ere shut taxa 23, 2011 likely Received September 12, 2011; Accepted November 1, 2011; Published November that are common in soil, the SourceTracker algorithm the most are Buildings are complex ecosystems that house trillions of microorganisms interactingSkin each with 40 ortion of other, with humans and with their environment. Understanding the ecological and evolutionary probably underestimates the relative importance of which permits always the most ß 2011 Flores et al. This is an[42,43]. Copyright: diligent of hand-washers open-access article distributed under the terms of the Creative Commons Attribution License, sources, like ORIGINAL ARTICLE Average contribution (%) Architectural design influences the diversity and structure of the built environment microbiome February 9, 2012 Do or Do in or ou t St all in Fa Sta uc et ll ou So han t ap d dis les pe ns To T e ile oile r tf lus t sea hh t a To ndle ile tf lo Si or nk flo or processes that determine the diversity and composition of the built environment microbiome—the unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. pant in indoor microbial community of microorganisms that live indoors—is important for understanding the relationship 20 Funding: This work was supported Foundation their Indoor Environment program, and ecology research,ofPeccia the Howard with funding from the Alfred P. Sloan had no role andstudy design, data collection and analysis, in part bytothe National between building design, biodiversity and human health. In this study, we used high-throughput Institutes Health and Hughes Medical Institute. The funders in decision publish, or sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and preparation of has thinks that the fieldthe manuscript. airborne bacterial communities at 0 health-care facility. We quantified airborne bacterial community a Competing Interests: structure and environmental conditions in patient rooms exposed to mechanical or window wh i c h yet to gel. And the Sloan The authors have declared that no competing interests exist. * E-mail: ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was 26 JanuFoundation’s Olsiewski lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments Journal, shares some of his concontained many taxa that are absent or rare outdoors, including taxa closely related to potential communities and revealed a greater diversity of bacteria on Introduction hanically cern. “Everybody’s genhuman pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative indoor surfaces than captured using cultivation-based techniques humidity and temperature, were correlated with the diversity and composition of indoor bacterial had lower erating vastMore than ever, individuals across the globe spend a large [10–13]. Most of the organisms identified in these studies are amounts of communities. The relative abundance of bacteria closely related to human pathogens was higher portion of their lives indoors, yet relatively little is known about the related to human are y than ones with openthan outdoors, and higher in rooms withquantify those con- lower relative humidity. looking across data sets 2. Relationship between bacterial communities associated with commensals suggesting that the organisms were they move around. But to lower airflow rates and data,” she says, but indoors winFigure ten public restroom surfaces. Communities microbial diversity of indoor environments. Of the studies that not actively The observed relationship between building design and airborne bacterial can be difficult because groups choose dif- of the unweighted UniFrac distance matrix. Each point represents agrowing on the surfaces but rather were deposited ility of fresh air translated tributions, Peccia’s team has had to develop diversity suggests that PCoA single sample. Note that the floor (triangles) and toilet (as have examined microorganisms associated with indoor environdirectly (i.e. touching) or indirectly (e.g. shedding of skin cells) by we can manage indoor environments, altering through building design and operation the community form tions of microbes associ- new methods to collect airbornemicrobiomeand our timeanalytical tools. With ments, most have relied upon cultivation-based techniques hands. humans. Despite these efforts, we still have an incomplete Sloan support, clusters distinct from surfaces touched with to of microbial species that potentially colonize the human bacteria during ferent indoors. doi:10.1371/journal.pone.0028132.g002 detect organisms residing on a variety of household surfaces [1–5]. The ISME Journal extract their DNA, 26 January 2012; are much understanding of bacterial communities associated with indoor an body, and consequently, advance online publication,as the microbesdoi:10.1038/ismej.2011.211 a data archive and integrated analytthough, Subject Category: microbial population and community ecology Not surprisingly, these studies have identified surfaces in kitchens environments because limitations of traditional 16 S rRNA gene high diversity communities is likely due to of related relative abundances of s pathogens. Although this less abundant in air than on surfaces. ical tools dispersal; Keywords: aeromicrobiology; bacteria; built environment microbiome; community ecology;are in the works. and restrooms as being hot of floorof bacterial contamination.the frequencyand sequencingdifferences in the made replicate sampling spots cloning techniques have e human ck to pre- contact shoes, which would track a diversity some surfaces (Figure 1B, Table notably environmental filtering In one recent study, they used air filters Because several pathogenic bacteria are known hat having natural airflow To foster collaborations between micro- with the bottom aofvariety of to survive on inand in-depth characterizations of abundant onS2). Most surfaces of microorganisms from sources including soil, which is were clearly more the communities prohibitive. certain surfaces for extended periods of time [6–8], these studies are of With the Green says answering that to sample airborne particles and microbes biologists, architects, and building scientists,in preventing the spread microbial habitat [27,39]. Indeed,advent of high-throughputrestrooms (Figure 1B). Some known to be a highly-diverse restrooms than male sequencing techniques, we obvious importance of human disease. can now bacteria commonly associated with soil (e.g. family indoor microbial communities at abun often most an Introduction microbiome—includes the foundation and comclinical data; she’s hoping in a classroom during 4 days during which human pathogensalso sponsored a symposium widely recognized that the majority of Rhodobacteraceae, investigate are the most common, andthe relationship However, it is now unprecedented depth and begin to understand mensals interacting with each other and with their Rhizobiales, Microbacteriaceae and Nocardioidaceae) were, on average, found in the vagina of healthy reproductive age w
  98. 98. Citizen Science
  99. 99. The Microbe Challenge • Microbes are small • But diversity and numbers are very high • Appearance not a good indicator of type or function • Field observations of limited value
  100. 100. The Microbe Era MICROBES RUN THE PLANET
  101. 101. MICROBES v
  102. 102. ??? ??? ??? MICROBES
  103. 103. MICROBES
  104. 104. Acknowledgements • GEBA: • $$: DOE-JGI, DSMZ • Eddy Rubin, Phil Hugenholtz, Hans-Peter Klenk, Nikos Kyrpides, Tanya Woyke, Dongying Wu, Aaron Darling, Jenna Lang • GEBA Cyanobacteria • $$: DOE-JGI • Cheryl Kerfeld, Dongying Wu, Patrick Shih • Haloarchaea • $$$ NSF • Marc Facciotti, Aaron Darling, Erin Lynch, • Phylosift • $$$ DHS • Aaron Darling, Erik Matsen, Holly Bik, Guillaume Jospin • iSEEM: • $$: GBMF • Katie Pollard, Jessica Green, Martin Wu, Steven Kembel, Tom Sharpton, Morgan Langille, Guillaume Jospin, Dongying Wu, • aTOL • $$: NSF • Naomi Ward, Jonathan Badger, Frank Robb, Martin Wu, Dongying Wu • Others (not mentioned in detail) • $$: NSF, NIH, DOE, GBMF, DARPA, Sloan • Frank Robb, Craig Venter, Doug Rusch, Shibu Yooseph, Nancy Moran, Colleen Cavanaugh, Josh Weitz • EisenLab: Srijak Bhatnagar, Russell Neches, Lizzy Wilbanks, Holly Bik