The Rise of the Microbiome talk by Jonathan Eisen for AHCJ15

1. The Rise of the Microbiome:
Challenges and Opportunities
ACHJ15
Jonathan A. Eisen
@phylogenomics
University of California, Davis

2. 0
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The Rise of the Microbiome

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

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Why Now?

5. Why Now I: Appreciation of Microbial Diversity
Functional Diversity
Diversity of Form
Phylogenetic Diversity
MICROBES
RUN THE
PLANET

6. Why Now II: Post Genome Blues
The Microbiome
Transcriptome
VariomeEpigenome
Overselling the Human Genome?

7. <<<<
Culturing Observation
CountCount
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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
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DNA
Why Now III: CSI-Microbiology Advances

8. Why Now IV: Sequencing Has Gone Crazy

9. Turnbaugh et al Nature. 2006 444(7122):1027-31.
Why Now V: Microbiome Functions

10. Challenge 1: Complexity
Microbial Diversity
Microbial Diversity2 Fragmented Data
Host Variation
http://bit.ly/HumanMicrobiome
Functional
Diversity

11. Challenge 1: Complexity
Host Variation
http://bit.ly/HumanMicrobiome
TranscriptomeSNPs, CNVs
Epigenetics
Environment

12. Challenge 2: Public Understanding
Germophobia Microbiomania

13. Opportunity 1: Better Reference Data

14. Opportunity 2: Better Methods
PhylOTU rRNA Copy # Correction Metagenomic PD
Genome TreePhyloSift PhyEco Markers
SFAMs Meta HiC Linking Taxa and Function

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. Mom The Microbes We Eat
PetsBuilt
Environment
Other People
Many Taxa
Opportunity 4: Whole Systems

17. Opportunity 6: Education & Outreach
http://microBE.net
http://gut-check.net

18. Opportunity 7: Citizen Science
Kitty Microbiome

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