How to keep up with microbial ecology and the built environment: microBEnet is your place

Just posting a wrap up of posts on microBEnet (where I blog frequently as do many other folks that work on something related to microbial ecology, the built environment, or the intersection of the two).  microBEnet is really becoming a central place to find out what is going on in the world of microbial ecology and the built environment.  And I love that we are getting more and more posts from outsiders about their work, their meetings, their ideas and more.  Anyway – here is a wrap up of the posts for the last month.  If you are interesting in joining microBEnet and writing posts about relevant topics, let me know.

Jenna Lang (staff scientist in my lab) — meeting reports from a Planetary Protection meeting

My posts:

Alexander Sczyrba on the Critical Assessment of Metagenome Interpretation (CAMI)

Elisabeth Bik from Stanford roundups from Microbiome Digest
David Coil (a staff scientist at UC Davis in my lab)
Linsey Marr of Virginia Tech
Rachel Adams – post doc at UC Berkeley
Ben Kirkup of the  Naval Research Laboratory
Embryete Hyde from UCSD

Brent Stephens of the Illinois Institute of Technology

Two Eisen lab papers selected for the PeerJ 2015 Collection

Cool.  Two paper from my lab were selected as highlights of 2014 papers in the Peer J: PeerJ Collection: PeerJ Picks 2015 Collection

The papers were

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

Jenna M. Lang,  Jonathan A. Eisen,  Angela M. Zivkovic


Aaron E. Darling,  Guillaume Jospin,  Eric Lowe,  Frederick A. Matsen,  Holly M. Bik,  Jonathan A. Eisen

Thanks PeerJ and all the co-authors for their great work.  I love open science and I particularly think we need continuing experiments on the best ways to do open science.  Thus I like the experiment that is PeerJ in regard to how to publish and how to pay for open access fees.

Full disclosure: I am an Academic Editor at PeerJ.

New lab paper: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

A new paper out from my lab (with Jenna Lang as the 1st author and in collaboration with Angela Zivcovic from the UC Davis Food For Health Initiative and the Department of Nutrition):  The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types.  The work in the paper focuses on characterizing the abundance and taxonomy of microbes in food from three model diets.

Basically, Angela prepared meals for these three diets

Food was purchased and prepared in a standard American home kitchen by the same individual using typical kitchen cleaning practices including hand washing with non-antibacterial soap between food preparation steps, washing of dishes and cooking instruments with non-antibacterial dish washing detergent, and kitchen clean-up with a combination of anti-bacterial and non-antibacterial cleaning products. Anti-bacterial products had specific anti-bacterial molecules added to them whereas “non-antibacterial” products were simple surfactant-based formulations. The goal was to simulate a typical home kitchen rather than to artificially introduce sterile practices that would be atypical of how the average American prepares their meals at home. All meals were prepared according to specific recipes (from raw ingredient preparation such as washing and chopping, to cooking and mixing).

And then she blended them and we characterzied the microbial communities in the blended samples:

After food preparation, meals were plated on a clean plate, weighed on a digital scale (model 157W; Escali, Minneapolis, MN), and then transferred to a blender (model 5,200; Vita-Mix Corporation, Cleveland, OH) and processed until completely blended (approximately 1–3 min). Prepared, ready to eat foods that were purchased outside the home were simply weighed in their original packaging and then transferred to the blender. 4 mL aliquots of the blended meal composite were extracted from the blender, transported on dry ice and then stored at −80 °C until analysis. The following analyses were completed using these meal composite samples: (1) total aerobic bacterial plate counts, (2) total anaerobic bacterial plate counts, (3) yeast plate counts, (4) fungal plate counts, and (5) 16S rDNA analysis for microbial ecology.

And Jenna Lang coordainted the sequence analysis and then Angela and Jenna (with some help here and there from me) coordianted the analysis of the different microbial data and the writing of the paper.

Figure 5: Biplot of taxa in sample PCoA space.

Lots of interesting things reported in the paper (read it, I insist).  I note – this is a demonstration project in a way – trying to get the community and others to think about the source pools of microbes that come into our system from our food.  It is by no means comprehensive or conclusive (read the caveats section of the paper).  Congrats to Jenna and Angela for all their hard work. Anyway – the paper is Open Access in PeerJ.  Eat it up.

UPDATE: Some press and blog coverage

Post-doc w/ me, Jessica Green, Jay Stachowicz, and Jenna Lang on seagrass microbiomes

Postdoctoral Position in Microbial Ecology and Evolution
Jessica Green at the University of Oregon Green ( is currently seeking a postdoctoral researcher to explore fundamental questions in microbial ecology and evolution. Applicants should have a PhD in a biological, computational, mathematical, or statistical field with extensive training using theory and/or modeling to understand the ecology and evolution of complex biological communities, and strong writing skills. Experience developing and applying quantitative phylogenetic ecological methods is highly desirable, but not explicitly required for candidates who have otherwise demonstrated strong quantitative skills.
The successful candidate will play a key role in the Seagrass Microbiome Project ( in collaboration among Jonathan Eisen, Jay Stachowicz, and Jenna Lang ( at the University of California, Davis. The Seagrass Microbiome Project aims to integrate the long interest in seagrass ecology and ecosystem science with more recent work on microbiomes to produce a deeper, more mechanistic understanding of the ecology and evolution of seagrasses and the ecosystems on which they depend. Our studies of the community of microorganisms that live in and on seagrasses – the seagrass “microbiome” – will contribute to a broader understanding of host-microbe systems biology, and will benefit from ongoing University of Oregon research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology ( and the Biology and Built Environment Center (
The position is available for 1 year with the possibility for renewal depending on performance. The start date is flexible. Please email questions regarding the position to Jessica Green (jlgreen).
To apply
A complete application will consist of the following materials:
(1) a brief cover letter explaining your background and career interests
(2) CV (including publications)
(3) names and contact information for three references
Submit materials to ie2jobs. Subject: Posting 14431
To ensure consideration, please submit applications by November 1, 2014, but the position will remain open until filled.
Women and minorities encouraged to apply. We invite applications from qualified candidates who share our commitment to diversity.
The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status.

What to do when you realize the meeting you are speaking at is a YAMMM (yet another mostly male meeting)?

I am supposed to be talking at a meeting Tuesday: Almaden Institute 2014: Sequence the City -Metagenomics in the Era of Big Data.

In looking at the agenda for the meeting I am pretty bummed about the gender ratio of speakers. Looks like 18:5 Men to Women. 

  • Jeff Welser IBM 
  • David Haussler UCSC 
  • Daniel Huson Tubingen U 
  • Joe DeRisi UCSF 
  • Jane Carlton NYU 
  • Ajay Royyuru IBM 
  • Paula Olsiewski Sloan Foundation 
  • Christopher Mentzel Moore Foundation 
  • Anne Marie Kimball Gates Foundation 
  • Jonathan Eisen UC Davis 
  • Jessica Green U Oregon 
  • Mark Adams JCVI 
  • Eric Alm MIT 
  • Raul Andino UCSF 
  • Scott Kahn Illumina 
  • Mike Lelivelt Ion Torrent 
  • Radoje (Rade) Drmanac Complete Genomics 
  • Brett Bowman Pacific Biosciences 
  • Chris Mason Cornell 
  • Bart Weimer UC Davis 
  • David Crean Mars 
  • Astri Wayadande Oklahoma State U 
  • Christopher Elkins FDA

Not sure what to do about this. I am certainly (in a few minutes) going to be writing to the organizers. I am also pondering cancelling talking. I try very hard to be vigilant about gender ratios at meetings and it drives me crazy to see such skews. I know it is not always possible to have meetings have equal representation and I know some people try very hard and do not succeed. But this seems unpleasantly extreme. So – any thoughts or recommendations as to what to do would be appreciated.

UPDATE 5/5 –

Well the schedule has been updated – and now the male: female speaker ratio is 21:6. Note – Jack Gilbert is moderating and speaking and I am counting him twice. Also Robert Prill is opening each day and closing day 2 so in a way this could be counted as 23:6.

  • Robert Prill, IBM 
  • Jeff Welser IBM 
  • David Haussler UCSC 
  • Daniel Huson Tubingen U 
  • Joe DeRisi UCSF 
  • Jane Carlton NYU 
  • Ajay Royyuru IBM 
  • Laurie Garrett (moderating) 
  • Paula Olsiewski Sloan Foundation 
  • Christopher Mentzel, Moore Foundation 
  • Anne Marie Kimball Gates Foundation 
  • Jonathan Eisen UC Davis 
  • Jessica Green U Oregon 
  • Robert Prill 
  • Mark Adams JCVI 
  • Eric Alm MIT 
  • Raul Andino UCSF 
  • Jack Gilbert (moderating) 
  • Jack Gilbert (speaking) 
  • Scott Kahn, Illumina 
  • Mike Lelivelt Ion Torrent 
  • Radoje (Rade) Drmanac Complete Genomics 
  • Brett Bowman Pacific Biosciences 
  • Chris Mason Cornell 
  • Bart Weimer UC Davis 
  • David Crean Mars 
  • Astri Wayadande Oklahoma State U 
  • Christopher Elkins FDA 
  • Robert Prill


So I decided to go to the meeting and talk. Here is a video slideshow of my talk with audio.

 and here are the slides on Slideshare

I am not sure if I made the right decision but what I decided to do was to change my talk to feature the work of women and to highlight those women.


Here are some pics showing the before (left) and after (right) for how I changed my talk from the previous talk I gave about this topic.  Among the changes I made:

  • I added names and pictures of the women behind the work 
  • Changed examples to be about work of women when I had been using work of men
  • Added additional examples of work by women directly related to my talk
And I used the pictures and names on the slides to remind me to talk about the women behind the work. 

I think this strategy is a potentially useful tool in combatting the implicit and subtle biases against women in STEM fields.  All of what I said was true.  I just made sure to emphasize and use examples of work by women when previously I had either not said who did certain work or had sometimes emphasized work by men.  And I made sure to show pictures and say the names of the women behind the work too.

Added name and picture of program officer Paula Olsiweski who I had quoted previously.
Changed example of new publication that we add to our collection and used a publication
by a female graduate student, post doc Rachel Adams.  
Included name and picture of student post-doc Rachel Adams on other slides
about the topic

Included name and picture of student post-doc Rachel Adams on other slides
about the topic. 

Added a mention of the blog post by student post-doc Rachel Adams.

Added picture and name of post doc Allison Fish who organized meeting
I was discussing.

Added name and picture of Mary Jo Seminoff who coordinates
production of the newsletter I had mentioned.

Added screenshot and names of Holly Bik interviewing Amy Pruden for the
“People Behind the Science” series mentioned in previous slide.

Added name and picture of Brooke Borel and discussed her news stories (had mentioned
news stories in general w/o examples)

Added picture and name and blog post of Holly Ganz who wrote about
the news stories by Brooke Borel.

Changed example to be about Maria Gloria Dominguez-Bello instead
of Thomas Bruns.

Changed example to be about Maria Gloria Dominguez-Bello instead
of Thomas Bruns.

Added extra slide discussing Software Carpentry workshop
organized by Jenna Lang and Tracy Teal (and added
names and pics of them).

Added pics and names of Jo Handelsman and Tiffany Tsang who coordinated
one of the examples on the slide but who had not gotten mentioned

Added picture and name of undergraduate student Hannah Holland-Moritz who was
involved in this work.

Added picture and name of research associate Madison Dunitz
who led this work.

Added name and picture of undergraduate student Sabreen Aulakh
who was involved in this work.

Added picture of graduate student Laura Sauder who
was our main contact in the lab of Josh Newfeld.

Added pictures and names of Darlene Cavalier and Caren Cooper who
inspired me to get involved in Citizen Science.

Added picture and name of Darlene Cavalier who was keynote speaker
at these meetings.

Added extra slide on the phone microbiome project and added names and pics of the people
involved including graduate student Georgia Barguil.

Added names and pics of the people behind this project (Holly Menninger and Rob Dunn)

Changed slide a little bit and added name and pic of Jessica Richman, one of the people behind the uBiome project.

Added pics that included more of the key women behind this project – including Darlene Cavalier, Wendy Brown
and Jenna Lang.

Added a slide about Altmetrics and added pic and name of Heather Piwowar and mentioned
her work  Had included one line about Altmetrics on a slide before.

Added reference to paper by Holly Bik and Miriam Goldstein and
emphasized the workshops run by Holly Bik.  Included pics and names on slide too.


Added links to find out more information about the work of the women in the slides (links are in the image captions).
UPDATE 9/6/14

Thanks to Software Carpentry (@swcarpentry) for coming to #UCDavis

Quick post here.  Jenna Lang in my lab has a post at microBEnet about the recent workshop that the Software Carpentry folks ran at UC Davis: Software Carpentry comes to UC Davis! | microBEnet: The microbiology of the Built Environment network.  It was a major success.  For those who don’t know Software Carpentry’s mission is is to build basic computing skills among researchers.  From their web site:

Software Carpentry helps researchers be more productive by teaching them basic computing skills. We run boot camps at dozens of sites around the world, and also provide open access material online for self-paced instruction. The benefits are more reliable results and higher productivity: a day a week is common, and a ten-fold improvement isn’t rare.

A great idea and done really well.  Others out there should consider hosting or attending one of their Boot Camps and checking out their materials on their web site.  See for example their videos and their reading list and their lessons.  They really do great things …

Crosspost: Woohoo – two more genome announcement papers from our undergraduate project on built environment reference genomes

Crossposting this from the microBEnet blog.
Two new papers out from the microBEnet Undergraduate Research: Built Environment Reference Genomes  project:
These go with two previously published ones:
And two more coming. So proud of the undergrads in my lab who did this work and David Coil for coordinating it with help from Jenna Lang and Aaron Darling.  Undergrads at UC Davis sequencing genomes of organisms they isolated. So cool.

Yes, the human microbiome has truly arrived: on Wait Wait Don’t Tell Me

So cool.  Yesterday on “wait wait … don’t tell me” Kai Penn (actor) was enticed to play the game “Ahhh! Get It Off Me!” in regard to microbes: Not My Job: Kal Penn Takes A Quiz On The Microbiome : NPR

Hat tip to Jenna Lang for pointing me to this.