The Microbiology of the Built Environment Network

http://microBE.net

Jonathan A. EisenUC Davis

@phylogenomics

Saturday, May 25, 13

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

microBEnet Targets

• Those funded by Sloan Program• Anyone in related fields w/ current or

potential interest in microBE• Stakeholders

Saturday, May 25, 13

microBEnet Activities

1.Web site/hub 2.Organizing meetings and workshops3.Creating and curating resources4.Social media activities 5.Teaching how to share

Saturday, May 25, 13

microBEnet Activities

• Ideas wanted

Saturday, May 25, 13

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

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

Undergrad projects

Saturday, May 25, 13

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

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

Undergrad Genome Project Blog

Saturday, May 25, 13

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 BharadwajHigh School:•Kevin Yang•In collaboration with Kenneth Kubo at American River College

Saturday, May 25, 13

Saturday, May 25, 13

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

Citizen Microbiology

• Workshop at UC Davis• ASM session (last week)• Multiple projects

Saturday, May 25, 13

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

Citizen Science

Saturday, May 25, 13

Crowdfunding/Crowdsourcing

Saturday, May 25, 13

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

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

Educate and Inform

Saturday, May 25, 13

Centralize Information

• Pull in blog posts and news from other sources

• Updates to social media• New papers• Twitter hashtag (#microbenet)

Saturday, May 25, 13

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

Reference Collections

• 102 members• 684 papers• Curated Tags

Saturday, May 25, 13

Other Information-Related

• Curate and analyze reference collections

• Simple guides• Sloan Program• Wikipedia curation

Saturday, May 25, 13

Sharing & Publicizing Sloan Work

Saturday, May 25, 13

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

Gaps

Saturday, May 25, 13

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

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