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A renewed need for a genomic field guide to microbes
This document discusses the need for a genomic field guide to microbes. It outlines several challenges to creating such a guide, including the small size and diversity of microbes, as well as difficulties observing and collecting data on them in natural environments. Potential solutions proposed include advances in DNA sequencing technologies that have enabled large-scale cataloging and identification of microbes. Components suggested for inclusion in a field guide are phylogenetic catalogs, functional profiles, biogeography data, identification methods, and information on applications like pathogen detection. Citizen science initiatives are also presented as a way to engage the public in microbiology. The talk concludes by advocating the creation of a comprehensive genomic field guide to microbes.
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A renewed need for a genomic field guide to microbes
- 1. A renewed needfor a genomic field guide to microbes April 23, 2021 Talk for BAEEID Bay Area Ecology and Evolution of Infectious Diseases Jonathan A. Eisen @phylogenomics University of California, Davis
- 2. A renewed needfor a genomic field guide to microbes April 23, 2021 Talk for BAEEID Bay Area Ecology and Evolution of Infectious Diseases Jonathan A. Eisen @phylogenomics University of California, Davis
- 3. BIRDS ARE AWESOME REALLYAWESOME April 23, 2021 Talk for BAEEID Bay Area Ecology and Evolution of Infectious Diseases Jonathan A. Eisen @phylogenomics University of California, Davis
- 4. Obsessed with Microbesfor a Long Time
- 5. Also a bitobsessed with birds …
- 6. First Biology Research- Hummingbirds at RMBL
- 7. Microbes Won, fora While
- 8. But I haveRediscovered My Love For Birds
- 9. But I haveRediscovered My Love Obsession For Birds
- 10. California Bird Observationson iNaturalist
- 11. California Bird Observationson iNaturalist
- 12. California Bird Observationson iNaturalist
- 13. The Bird -Microbe Connection • Important to note … I rediscovered my obsession with birds directly due to my work on microbes
- 14. • Important tonote … I rediscovered my obsession with birds directly due to my work on microbes The Bird - Microbe Connection Walter Boyce Holly Ganz Sarah Hird
- 15. The Bird -Microbe Connection • Important to note … I rediscovered my obsession with birds directly due to my work on microbes Walter Boyce Holly Ganz Sarah Hird Ladan Daroud Alana Firl
- 16. The Bird -Microbe Connection
- 17. 2004 Bird Sighting photoby J. Eisen
- 18. photo by J.Eisen 2004 Bird Sighting
- 19. People Got Excited photoby J. Eisen
- 20. What Bird IsThis?
- 21. Field Guide tothe Birds of North America photo by J. Eisen
- 22. Field Guide tothe Birds of North America photo by J. Eisen
- 23. Field Guide tothe Birds of North America photo by J. Eisen
- 24. iBird photo by J.Eisen
- 25. Get Some HelpWith ID - Taken Wednesday in my yard
- 27. AI System SuggestsID Based on Location
- 28. AI System SuggestsID Based on Location
- 29.
- 30.
- 31. Back to theBird …
- 32.
- 33.
- 51. ! Phylogenetic catalogof types of organism ! Functional diversity ! Biogeography (space and time) ! Niche and in situ function ! Means for identification • Provides a guide to interpret normal states and abnormalities ! Emerging pathogens ! Enzyme Discovery ! Microbial Forensics ! Climate Change ! Antimicrobial resistance ! Genetic manipulation ! Bioweopons release ! Vaccine design
- 52. MICROBES DO IT We NeedA Field Guide to the Microbes
- 53. MICROBES CRAZY We Need AField Guide to the Microbes
- 54. 2004: “Global FieldGuide for Microorganisms”
- 55. 2009 - Callfor a Genomic Field Guide to Microbes
- 56.
- 57. Challenge I: Small,Hard to Study in Field • Microscope picture • Microbes are small • But diversity and numbers are very high • Appearance not a good indicator of type or function • Field observations of limited value
- 58. Challenge II: Diversityof Form
- 59. Challenge III: Diversityof Functions The Bad The Good The Unusual The Consumable The Burnable The Planet
- 60. Challenge IV: EvolutionaryDiversity Viruses Bacteria & Archaea Fungi Other Eukaryotes
- 61. Challenge V: MicroscaleLocalization Jessica L. Mark Welch, Blair J. Rossetti, Christopher W. Rieken, Floyd E. Dewhirst, and Gary G. Borisy PNAS February 9, 2016. 113 (6) E791-E800; published ahead of print January 25, 2016. https://doi.org/10.1073/pnas.1522149113 Jessica L. Mark Welch, Blair J. Rossetti, Christopher W. Rieken, Floyd E. Dewhirst, and Gary G. Borisy PNAS February 9, 2016. 113 (6) E791-E800; published ahead of print January 25, 2016. https:// doi.org/10.1073/pnas.1522149113
- 62. <<<< Culturing Observation Count Count http://www.google.com/url? sa=i&rct=j&q=&esrc=s&source=images& cd=&docid=rLu5sL207WlE1M&tbnid=CR LQYP7d9d_TcM:&ved=0CAUQjRw&url=h ttp%3A%2F%2Fwww.biol.unt.edu%2F~jaj ohnson%2FDNA_sequencing_process&e i=hFu7U_TyCtOqsQSu9YGwBg&psig=AF QjCNG-8EBdEljE7- yHFG2KPuBZt8kIPw&ust=140487395121 1424 DNA Challenge VI:Collecting Data The Great Plate Count Anomaly
- 63. MICROBES CRAZY We Need AField Guide to the Microbes
- 64. MICROBES POSSIBLE? We Need AField Guide to the Microbes
- 65. Solutions to Challenges •Scientific solutions • Engagement solutions
- 66. • Scientific solutions •Engagement solutions Solutions to Challenges
- 67. Science Solution I:DNA Sequencing
- 68. 2002-2007: TIGR Treeof Life Project Figure from Barton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree Naomi Ward Kare n Nelson
- 69. 2007-2014: GEBA Figure fromBarton, Eisen et al. “Evolution”, CSHL Press based on Baldauf et al Tree
- 70.
- 71. SARS-CoV-2 Origins /PREDICT Wells et al. 2021
- 72. Components of aField Guide • What should be included ! Phylogenetic catalog of types of organism ! Functional diversity ! Biogeography (space and time) ! Niche and in situ function ! Means for identification • Provides a guide to interpret normal states and abnormalities ! Emerging pathogens ! Enzyme Discovery ! Microbial Forensics ! Climate Change ! Antimicrobial resistance ! Genetic manipulation ! Bioweopons release ! Vaccine design
- 73. Environmental Sequencing 9 Supplementary Figures 31 32 Fig.S1 Map depicting soil collection locations for greenhouse experiment. 33 10 234 Fig. S2. Sampling and collection of the rhizocompartments. Roots are collected from rice 235 plants and soil is shaken off the roots to leave ~1mm of soil around the roots. The ~1 mm of soil 236
- 74. Components of aField Guide • What should be included ! Phylogenetic catalog of types of organism ! Functional diversity ! Biogeography (space and time) ! Niche and in situ function ! Means for identification • Provides a guide to interpret normal states and abnormalities ! Emerging pathogens ! Enzyme Discovery ! Microbial Forensics ! Climate Change ! Antimicrobial resistance ! Genetic manipulation ! Bioweopons release ! Vaccine design
- 75. Other Science Solutions:Other Advances
- 76. Components of aField Guide • What should be included ! Phylogenetic catalog of types of organism ! Functional diversity ! Biogeography (space and time) ! Niche and in situ function ! Means for identification • Provides a guide to interpret normal states and abnormalities ! Emerging pathogens ! Enzyme Discovery ! Microbial Forensics ! Climate Change ! Antimicrobial resistance ! Genetic manipulation ! Bioweopons release ! Vaccine design
- 77. • Scientific solutions •Engagement solutions Solutions to Challenges
- 78. Engage I: CitizenMicrobiology Kitty Microbiome Jack Gilbert Project MERCCURI Phone and Shoes tinyurl/kittybiome Holly Ganz
- 79.
- 80. Components of aField Guide • What should be included ! Phylogenetic catalog of types of organism ! Functional diversity ! Biogeography (space and time) ! Niche and in situ function ! Means for identification • Provides a guide to interpret normal states and abnormalities ! Emerging pathogens ! Enzyme Discovery ! Microbial Forensics ! Climate Change ! Antimicrobial resistance ! Genetic manipulation ! Bioweopons release ! Vaccine design
- 81. MICROBES POSSIBLE We Need AField Guide to the Microbes
- 82. No Birds AreBoring
- 83. No Microbes AreBoring
- 84. MICROBES LET’S DO IT WeNeed A Field Guide to the Microbes
- 85.