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The Rise of the Microbiome - talk by Jonathan Eisen for AHCJ15

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The Rise of the Microbiome talk by Jonathan Eisen for AHCJ15

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The Rise of the Microbiome - talk by Jonathan Eisen for AHCJ15

  1. 1. The Rise of the Microbiome: Challenges and Opportunities ACHJ15 Jonathan A. Eisen @phylogenomics University of California, Davis
  2. 2. 0 1000 2000 3000 4000 00 01 02 03 04 05 06 07 08 09 10 11 12 13 Pubmed “Microbiome” Hits The Rise of the Microbiome
  3. 3. microBIOME or microbiOME • microbi-OME collection of genomes of microbes from a community (emphasis on OME) • micro-BIOME a community of microbes (emphasis on BIOME) • see http://tinyurl.com/definemicrobiome
  4. 4. 0 1000 2000 3000 4000 00 01 02 03 04 05 06 07 08 09 10 11 12 13 Pubmed “Microbiome” Hits Why Now?
  5. 5. Why Now I: Appreciation of Microbial Diversity Functional Diversity Diversity of Form Phylogenetic Diversity MICROBES RUN THE PLANET
  6. 6. Why Now II: Post Genome Blues The Microbiome Transcriptome VariomeEpigenome Overselling the Human Genome?
  7. 7. <<<< Culturing Observation CountCount http://www.google.com/url?sa=i&rct=j&q=& esrc=s&source=images&cd=&docid=rLu5s L207WlE1M&tbnid=CRLQYP7d9d_TcM:& ved=0CAUQjRw&url=http%3A%2F%2Fw ww.biol.unt.edu%2F~jajohnson%2FDNA_ sequencing_process&ei=hFu7U_TyCtOqs QSu9YGwBg&psig=AFQjCNG-8EBdEljE7- yHFG2KPuBZt8kIPw&ust=140487395121 1424 DNA Why Now III: CSI-Microbiology Advances
  8. 8. Why Now IV: Sequencing Has Gone Crazy
  9. 9. Turnbaugh et al Nature. 2006 444(7122):1027-31. Why Now V: Microbiome Functions
  10. 10. Challenge 1: Complexity Microbial Diversity Microbial Diversity2 Fragmented Data Host Variation http://bit.ly/HumanMicrobiome Functional Diversity
  11. 11. Challenge 1: Complexity Host Variation http://bit.ly/HumanMicrobiome TranscriptomeSNPs, CNVs Epigenetics Environment
  12. 12. Challenge 2: Public Understanding Germophobia Microbiomania
  13. 13. Opportunity 1: Better Reference Data
  14. 14. Opportunity 2: Better Methods PhylOTU rRNA Copy # Correction Metagenomic PD Genome TreePhyloSift PhyEco Markers SFAMs Meta HiC Linking Taxa and Function
  15. 15. Opportunity 3: Model Systems (e.g., Rice) Edwards et al. 2015. Structure, variation, and assembly of the root-associated microbiomes of rice. PNAS Variation w/in Plant Cultivation Site Effects Rice Genotype Effects Function x Genotype Time Series
  16. 16. Mom The Microbes We Eat PetsBuilt Environment Other People Many Taxa Opportunity 4: Whole Systems
  17. 17. Opportunity 6: Education & Outreach http://microBE.net http://gut-check.net
  18. 18. Opportunity 7: Citizen Science Kitty Microbiome
  19. 19. Acknowledgements DOE JGI GBMF DARPA Aaron Darling Russell Neches Rob Knight Tanja Woyke Jessica Green Darlene Cavalier Eddy Rubin Dongying Wu Phil HugenholtzSundar Srijak Bhatnagar Jennifer Gardy Holly Ganz

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