Talk by Jonathan Eisen about microBEnet for 2013 meeting of the Sloan Foundation program on microbiology of the built environment

1. The Microbiology of the
Built Environment Network
http://microBE.net
Jonathan A. Eisen
UC Davis
@phylogenomics
Saturday, May 25, 13

2. microBEnet: Who?
• UC Davis:
• Jonathan Eisen
• David Coil
• Mary Jo Seminoff
• Holly Bik
• Tom Olson
• Russell Neches
• Jenna Lang
• many undergrads
• Building Ecology Research Group:
• Hal Levin
• Other collaborators
• Jessica Green
• Jack Gilbert, Dan Smith, others at Argonne and U. Chicago
• Darlene Cavalier, Wendy Brown, Mark Severance, Summer
Williams
Saturday, May 25, 13

3. microBEnet Targets
• Those funded by Sloan Program
• Anyone in related fields w/ current or
potential interest in microBE
• Stakeholders
Saturday, May 25, 13

4. microBEnet Activities
1.Web site/hub
2.Organizing meetings and workshops
3.Creating and curating resources
4.Social media activities
5.Teaching how to share
Saturday, May 25, 13

5. microBEnet Activities
• Ideas wanted
Saturday, May 25, 13

6. Future (ideas from 2012 Mtg)
• Host resources that others have that
could be helpful to share
• Guest blog posts
• Latest papers with background
• More targeted workshops to develop
interactions
• Undergrad education
• K-12 outreach
• Public outreach
Saturday, May 25, 13

7. Future (ideas from 2012 Mtg)
• Host resources that others have that
could be helpful to share
• Guest blog posts
• Latest papers with background
• More targeted workshops to develop
interactions
• Undergrad education
• K-12 outreach
• Public outreach
Saturday, May 25, 13

8. Undergrad projects
Saturday, May 25, 13

9. Why Undergrad Projects
• Undergraduate research projects in the
built environment
• A form of outreach (blogging, etc)
• Develop teaching materials related to the
microbiology of the built environment
• Keep our lab in the loop
• A touch of useful data
Saturday, May 25, 13

10. Reference Genomes
• 7 students
• Cultured organisms
isolated from a variety of
built environments
• Identify, sequence,
assemble, annotate,
publish a genome each
• 5 papers published so far in
Genome Announcements
• All Data released
• Student blog
•Brachybacterium muris
(Jonathon Lo):
•Microbacterium sp (Zach
Bendiks):
•Curtobacterium flaccumfaciens
(Jennifer Flanagan)
•Dietzia sp (Amanda Diep):
•Kocuria rosea (Jessica Doctor):
•Leucobacter sp (Dakota Bevans,
Hannah Holland-Moritz):
Saturday, May 25, 13

11. Undergrad Genome Project Blog
Saturday, May 25, 13

12. Aquarium Biogeography
• 6 students
• 16S surveys and
metagenomics in aquariums
• Looking at biogeography
and succession
• Using MBE tools
• Paper in progress
• Coordinated by Jenna Lang,
David Coil, Matt Haggerty
Undergraduates:
•Sabreen Aulakh
•Alex Alexiev
•Akshay Sethi
•Andrew Shaver
•Jennifer Flanagan
•Lakshmi Bharadwaj
High School:
•Kevin Yang
•In collaboration with Kenneth
Kubo at American River
College
Saturday, May 25, 13

13. Saturday, May 25, 13

14. Future (ideas from 2012 Mtg)
• Host resources that others have that
could be helpful to share
• Guest blog posts
• Latest papers with background
• More targeted workshops to develop
interactions
• Undergrad education
• K-12 outreach
• Public outreach
Saturday, May 25, 13

15. Citizen Microbiology
• Workshop at UC Davis
• ASM session (last week)
• Multiple projects
Saturday, May 25, 13

16. Project MERCCURI
• Sample International Space Station in
collaboration with Nanoracks
• Outreach by sampling at various public
events
• Collaboration with Science
Cheerleaders and Science for Citizens
• Darlene Cavalier, Summer Williams,
Mark Severance
• UCD: David Coil, Jenna Lang, Russell
Neches, et al.
Saturday, May 25, 13

17. Citizen Science
Saturday, May 25, 13

18. Crowdfunding/Crowdsourcing
Saturday, May 25, 13

19. Future (ideas from 2012 Mtg)
• Host resources that others have that
could be helpful to share
• Guest blog posts
• Latest papers with background
• More targeted workshops to develop
interactions
• Undergrad education
• K-12 outreach
• Public outreach
Saturday, May 25, 13

20. Future (ideas from 2012 Mtg)
• Host resources that others have that
could be helpful to share
• Guest blog posts
• Latest papers with background
• More targeted workshops to develop
interactions
• Undergrad education
• K-12 outreach
• Public outreach
Saturday, May 25, 13

21. Educate and Inform
Saturday, May 25, 13

22. Centralize Information
• Pull in blog posts and news from
other sources
• Updates to social media
• New papers
• Twitter hashtag (#microbenet)
Saturday, May 25, 13

23. Monthly Newsletter
• Summary of
blog posts
• “Resource of
the Month”
• “People Behind
the Science”
video series…
“Project of the
Month”
• Recent and
upcoming
meetings
Saturday, May 25, 13

24. Reference Collections
• 102 members
• 684 papers
• Curated Tags
Saturday, May 25, 13

25. Other Information-Related
• Curate and analyze reference
collections
• Simple guides
• Sloan Program
• Wikipedia curation
Saturday, May 25, 13

26. Sharing & Publicizing Sloan Work
Saturday, May 25, 13

27. Sharing & Publicizing Sloan Work
• Guest blog posts
• microBEnet posts
• Mendeley
• Video interviews
• Press
• Data sharing
• Pre and post publication
• Job postings
• Networking
Saturday, May 25, 13

28. Gaps
Saturday, May 25, 13

29. Gaps
• Citizen microbiology
• QIIME/VAMPS use
• Software Carpentry
• Culture collections
• Genomes of isolates
• How to share
• Methods sharing
• Other related social media
• Alt metrics
• Simulated community samples
Saturday, May 25, 13

30. Thanks
• Alfred P. Sloan Foundation
• microBEnet people: Hal Levin, David Coil, Mary Jo
Seminoff, Holly Bik, Jenna Lang, Russell Neches, Tom
Olson, et al
• All the undergrads in the lab
• Science Cheerleaders and Science for Citizens esp.
Darlene Cavalier, Wendy Brown, Mark Severance,
Summer Williams
• Collaborators: Jessica Green, Jack Gilbert, Dan
Smith, et al.
• Sloan Funded researchers / labs
• Others working in microBE topics
• Advice: Rob Dunn, Holly Menninger, Rob Knight,
manyothers
Saturday, May 25, 13