Slides for my talk at the 2019 ADVANCE Scholar Award Symposium. Talk covered a little bit about mt research and more about STEM Diversity. See https://diversity.ucdavis.edu/2019-advance-scholar-award-symposium

1. ########
#STEMDiversity #YAMMM #Manels #ClosedAccess
The power and peril of social media in improving the
culture and practice of science
October 24, 2019
UC Davis ADVANCE Symposium
Jonathan A. Eisen
@phylogenomics
University of California, Davis

2. Microbiomes: Communities of Microbes
Image by Darryl Leja, NHGRI

3. Microbiomes: Mostly Ignored but Not Anymore
Image by Darryl Leja, NHGRI

4. Google Trends Hits to Microbiome
The Rise of the Microbiome

5. The Rise of the Microbiome
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Pubmed Hits to Microbiome vs. Year

6. Why Now I: Appreciation of Microbial Diversity

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

8. Why Now III: Technological Advances

9. Why Now III: Technological Advances

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

11. Why Now IV: Microbiome Functions
Turnbaugh et al Nature. 2006 444(7122):1027-31.
#1: Microbiome impacts key trait
#2: Microbiome is transferable / modifiable

12. Why Now V: Importance of Other Microbiomes

13. 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

14. Challenge II: Diversity of Form

15. Challenge III: Diversity of Functions
The Bad The Good The Unusual
The Consumable
The Burnable The Planet

16. Challenge IV: Evolutionary Diversity
Viruses
Bacteria & Archaea
Other Eukaryotes
Fungi

17. Challenge V: Microscale Localization
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

18. Microbiomes: Communities of Microbes
Image by Darryl Leja, NHGRI

19. Solution for Eisen Lab: DNA Sequencing

20. Eisen Lab

21. Eisen Lab
Jonathan Eisen’s Lab
May the Microbes Be Ever in Your Favor
A
B
C
Input Sequences
rRNA workflow
protein workflow
profile HMMs used to align
candidates to reference alignment
Taxonomic
Summaries
pa
rallel op
tio
n
hmmalign
multiple alignment
LAST
fast candidate search
pplacer
phylogenetic placement
LAST
fast candidate search
LAST
fast candidate search
search input against references
hmmalign
multiple alignment
hmmalign
multiple alignment
Infernal
multiple alignment
LAST
fast candidate search
<600 bp
>600 bp
Sample Analysis &
Comparison
Krona plots,
Number of reads placed
for each marker gene
Edge PCA,
Tree visualization,
Bayes factor tests
eachinputsequencescannedagainstbothworkflows

22. UC Davis Microbiome Special Research Program
• 2 year Special Research Program funded by the Office of
Research and multiple campus Colleges
• Goal: catalyze development and innovation in microbiome
research on campus
• 1: Catalyze research through seed funding programs
• 2: Virtual hub for UCD Microbiome Research
• 3: Organize quarterly meetings

23. Microbiomania vs. Germophobia
Germophobia Microbiomania

24. Microbiomania vs. Germophobia
Germophobia Microbiomania
All Microbes Are Bad
Use Antimicrobials
in Everything
Avoid all Microbes
All Microbes Are Good
Use Probiotics
in Everything
Embraces all Microbes
Eat Dirt

25. Solution I: Citizen Microbiology
Kitty Microbiome
Jack Gilbert
Project MERCCURI
Phone
and
Shoes
tinyurl/kittybiome
Holly Ganz

26. Solution II: Outreach
http://gut-check.net

27. Engage: Example

33. Diversity in STEM #DoSomething

34. Lesson 1: Organizations Can Change
• Linda Katehi
• Maureen Stanton
• Linda Bisson
• Kimberlee Shauman
• Denneal Jamison-McClung

35. Lesson 2: Public Representation Matters

36. Lesson 2: Public Representation Matters

37. Lesson 2: Public Representation Matters

38. Lesson 3: Sexual Harassment & Assault is Pervasive

39. Lesson 3: Sexual Harassment & Assault is Pervasive

40. Lesson 3: Sexual Harassment & Assault is Pervasive

41. Lesson 4: Listen and Amplify Voices of Others

42. Lesson 4: Listen and Amplify Voices of Others

43. Lesson 5: UC Davis Rules

44. Lesson 5: UC Davis Rules
Deb Niemeier, Ph.D.
Colleen E. Clancy
Sarah McCullough
Maureen Stanton

45. Other Lessons

46. Other Lessons
• Lesson 6: Tech Industry Needs To Change
• Lesson 7: Not Just One Angle On Diversity
• Lesson 8: Use Your Privilege
• Lesson 9: Never Kick Down
• Lesson 10: Apologize When Wrong …

47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Lokiarchaea named after Loki’s Castle Vent Site

48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Thorarchaeota
http://sites.utexas.edu/baker-lab/2016/01/29/introducing-thorarchaeota/

49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Asgard Archaea

50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Asgard Archaea
Something is Wrong Here

51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Complaining on Twitter …

52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Response ..

53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Helarchaeota

54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Freya not next ..

55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Helarchaeota

56. Eisen Lab