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

• Planetary Protection Workshop (Forward Contamination)
• Workshop on Planetary Protection Knowledge Gaps for Human Extraterrestrial Missions (Intro)

My posts:

• Is the MinION thumb drive sequencer taking off? Seems so …
• Interesting analysis of data sharing in paleogenetics #OpenScience
• Great “Hidden Life” (of homes and people) Learning Activity from the NY Times #microbiology
• Important read from Aaron Darling: Not so fast, FastTree
• Fascinating and distressing look at cruise ship turnaround
• Resistance (The Film) coming to UC Davis April 9
• Great #openaccess collection of papers on RNA
• Today in germophobia and antimicrobiomism: grandparents who hate microbes
• I love that @eLIFE is publishing draft papers now (brewery microbiome)
• Evolution of DNA Sequencing 2015 Version
• Methylisothiazolinone in household items – a growing (or well, killing) problem #germophobia
• Cool: James Clemens High School-Hudson Alpha Classroom Microbiome Project
• Well, I guess this means microbiome engineering has arrived (sort of)
• Today in “where’s the pathogen?” Can you find Burkholderia on 500 acres with 50 samples?
• Yes Virginia, there is a paper on microbial transfer during beer pong
• Healthy Buildings 2015 meeting promo / preview

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

• CAMI Challenge is Now Open for Participation

Elisabeth Bik from Stanford roundups from Microbiome Digest

• Best of MicrobiomeDigest: Fisherman’s Friends
• MicrobiomeDigest – your daily fix of microbiome literature

Greg Caporaso from Northern Arizona University on SciPy

• SciPy 2015 Computational Life and Medical Sciences Mini-Symposium: Call for Abstracts

David Coil (a staff scientist at UC Davis in my lab)

• Official release of Gut Check: The Microbiome Game “print-at-home” edition
• Nostra culpa: Revised results for the microbial playoffs in space
• Gizmodo article regarding discussing data uncertainty in microbiome studies

Bill Van Bonn (of the Shedd Aquairum)  on the Aquarium Microbiome Project

• The Built Aquatic Environment

Linsey Marr of Virginia Tech

• What sequencing core do you recommend for environmental samples with low concentrations?

Alex Alexiev - undergraduate in my lab

• Microbes Corroding Concrete
• Using Sewage to Estimate a City’s Gut Health?

Maria Nunez of Mycoteam

• Microbial sampling in building surveys: what and why are we sampling?

Amanda Makowiecki at UC Boulder

• Acquired Resistance to Ultraviolet Germicidal Irradiation

Rachel Adams - post doc at UC Berkeley

• Fungal amplicons

Ben Kirkup of the  Naval Research Laboratory

• Bad-omics

Embryete Hyde from UCSD

• Rob Knight’s lab moves to UCSD
• Rob Knight’s TED Talk Released!

Brent Stephens of the Illinois Institute of Technology

• Building science measurements in the Hospital Microbiome Project: Part 2

Bubba Brooks from UC Berkeley

• New paper on diseased vs healthy infants in a NICU, possible impacts for future hospital microbiome work

Kyle Bibby of the University of Pittsburg

• The Pittsburgh Water Microbiome Project

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

and 

PhyloSift: phylogenetic analysis of genomes and metagenomes

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

• Kevin Bonham on SciAM Blogs: The Microbes in Your Kitchen (Or in your Starbucks mocha)
• Maddie Stone on Motherboard: Here’s How Many Microbes You Eat in a Single Day
• “This paper will hopefully convince the powers that be that the next study, actually looking at how different foods or diets with differing microbes affect people, should be funded soon,” Zivkovic told me.
• Nathan Gray:  The microbes we eat: Study investigates bacteria in different diets
• Ross Pomeroy on Real Clear Science: This Is How Many Microbes You'll Eat Today
• Improbable Research: What’s Eating You, and/or Vice Versa: Microbes
• Marissa Fessenden at Smithsonian: You Eat Millions...Even Billions!...of Microbes Every Day

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 (http://pages.uoregon.edu/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 (http://seagrassmicrobiome.org) in collaboration among Jonathan Eisen https://phylogenomics.wordpress.com), Jay Stachowicz http://www-eve.ucdavis.edu/stachowicz/stachowicz.shtml, and Jenna Lang (http://jennomics.com/) 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 (http://meta.uoregon.edu/) and the Biology and Built Environment Center (http://biobe.uoregon.edu/).

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.