Category: Meetings

Lake Arrowhead Microbial Genomics

Lake Arrowhead

Postdoc Roxana Hickey presented “Microbial interactions between humans and the built environment” at the 21st Lake Arrowhead Microbial Genomics meeting held in Lake Arrowhead, California on September 18-22, 2016 (slide deck below). The biannual conference hosted more than 100 scientists and featured a variety of speakers (58% of whom were female!) highlighting research on the human microbiome, disease pathogenesis, population and evolutionary genomics, and cutting-edge omics techniques. Jonathan Eisen (UC Davis), a long-time attendee and promoter of the meeting, chaired a session on the built environment microbiome (Storify here) in which Dr. Hickey presented past and present BioBE research. Other talks in the session included microbial community assembly in cheese manufacturing (Rachel Dutton, UC San Diego), a citizen science study of the highly polluted Gowanus Canal in New York City (Elizabeth Hénaff, Mason lab @ Weill Cornell Medicine), community engagement through microbiome research aboard the International Space Station (David Coil, Eisen lab @ UC Davis), and evolution of biofilm formation in response to rising marine temperature (Alyssa Kent, Adam Martiny lab @ UC Irvine).


David Coil summarized each day of talks at the meeting on the microBEnet blog (day 1, 2, 3 and 4), and Jonathan Eisen created several Storify recaps of #LAGM16 tweets (here, here and here). The meeting was the most Twitter-active I (Roxana Hickey) have attended and contributed to yet, which facilitated active discussions with members both at and away from the meeting.

Here are my main three main takeaways from the meeting:

  1. Metagenomics (and other ‘omic’ techniques) is gaining strength and popularity for a variety of applications. These include genome reconstruction across whole communities of microorganisms, strain-level diversity and population genomics, functional analyses, and development of targeted therapeutics and rational probiotics. There were very few amplicon-based studies at this meeting (I noticed a similar trend at the International Symposium on Microbial Ecology #ISME16 last month in Montreal). In addition, the tools used to analyze omics data are plentiful and sophisticated. I was especially impressed by work featured from the labs of Eric Alm (MIT), Jill Banfield (UC Berkeley), Kostas Konstantinidis (Georgia Tech), and Adam Phillippy (NIH).
  2. Many are beating the drum for more reference genomes and cultured isolates. Human-associated bacteria are fairly well-represented in the databases, thanks in large part to the Human Microbiome Project, but for most other environments we have relatively low representation of the resident microbes. This dearth of reference genomes limits our ability to make inferences about the function and ecology of the vast majority of microbes on earth, as was highlighted in a recent update to the tree of life (Hug et al. Nature 2016). More and more scientists are shifting some of their efforts toward cultivation and sequencing of isolates from diverse environments.
  3. Citizen science and community outreach are increasingly popular and wildly successful approaches to microbiome research. I was really excited to learn about the BKBioreactor Project on the Gowanus Canal (which made use of a community biohacker lab in Brooklyn), Project MERCCURI (which relied on crowdsourcing efforts to send microbes to space), and FijiCOMP (a really cool study looking at microbial transmission among members of a community in Fiji). All of these projects promote open access to data and publications. It got me very excited and thinking about ways to incorporate more public outreach in my own research.

Finally, I would be remiss not to mention the stunning fluorescence microscopy images of dental plaque presented by Jessica Mark Welch (Marine Biological Laboratory) illustrating genus-specific bacterial assemblages in the finest of detail (recently published in PNAS). These images are not only beautiful, but they also provide direct insights into physical interactions between populations of bacteria and inform hypotheses about their possible ecological roles in assembly and succession. Would love to see this technique employed in other microbial habitats!

2016 Pacific Northwest Women in Science Retreat


I (Ashley Bateman) recently won a scholarship from the Women in Graduate Sciences organization at the University of Oregon, to attend the 2016 Pacific Northwest Women in Science Retreat. The event was held at Camp Magruder in Rockaway Beach, OR from July 8th-10th. The attendees and workshop leaders featured over 100 women from across the STEM career spectrum, from graduate students, technicians, and post-docs to government and industrial early and late career scientists. The focus of this retreat is on professional skill development and professional networking, especially for and with other women scientists in the region. The retreat featured 3 main workshops: A COACh workshop on the Performing Art of Science Presentations, a Rehearsals for Life: workshop, and a Bragging workshop led by the enthusiastic Judy Giordan. We also heard from and asked questions of a diverse group of women on academic, industrial, and alternative career panels.

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Clarisse Betancourt and Gwynne Mhuireach received scholarships to attend the Healthy Buildings America 2015

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Clarisse Betancourt Román and Gwynne Mhuireach have both been awarded scholarships to attend and present their research at the Healthy Buildings 2015 America Conference in Boulder, CO, July 19-22. The mission of the conference is to promote collaboration among built environment researchers and practitioners in order to make buildings healthier and more sustainable. Clarisse and Gwynne will be presenting in a special session focused on Urban and Indoor Environments.

AIA Design & Health Research Consortium Kickoff

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G.Z. Brown of BioBE and Deb Johnson-Shelton of the Oregon Research Institute attended the kickoff meeting of the AIA Design & Health Research Consortium on March 5, 2015.  Held at the Robert Wood Johnson Foundation in Princeton, New Jersey, the 11 inaugural university members of the consortium heard from several invited speakers from the fields of architecture and public health. Table discussions were held around the topics of education, metrics, the “internet of things”, resilience and equity, and translation. More on the consortium can be found at

Erica Hartman is selected as recipient of the 2015 Donald E. Wimber Fund Award


The Donald E. Wimber Fund Award was created through the generosity of Carol Cogswell as a memorial to retired University of Oregon biology faculty member Donald Wimber. The award was established to provide support for junior faculty, research associates, or graduate students to travel to conferences to present their research work. Erica will be traveling to ASM.

3rd Annual Microbiology of the Built Environment Conference


Last week several members of the BioBE Center visited Boulder, CO for the 3rd annual Microbiology of the Built Environment Conference hosted by the Alfred P. Sloan Foundation. James Meadow presented our recent work on building-scale microbial patterns, the phone-hand connection, and the human microbial cloud. Adam Altrichter presented a poster (see it here) on our ongoing work with the Light Box experiments that Kyla Martichuski put together for a recent symposium at the U of O. Gwynne Mhuireach also presented a poster with an update on the analyses from her study looking at the bacteria in air from parks vs parking lots throughout Eugene. Check out the Storify put together from tweets during the conference to see what folks were talking about all week.

AAAS Meeting on Microbiomes of the Built Environment

Last week a AAAS meeting on the Microbiomes of the Built Environment was held to bring together leaders in the field to discuss existing knowledge and future directions. Jessica Green participated in the panel video above and the whole meeting is available online.

You can also check out the Storify of tweets during the meeting created by Jonathan Eisen.

Meta-Analysis of Indoor Biome Datasets – A New Collaboration!

This past September, Sloan-funded biologists Ashley Bateman, James Meadow, Rachel Adams, and Holly Bik met at UC-Berkeley to begin collaboration on an exciting new project!

The past few years have seen a dramatic increase in the number of microbiological studies undertaken in the indoor environment. It seems that these studies have arrived at the same general conclusions regarding microbial richness and diversity, but they also suggest that different processes are structuring microbiological communities differently depending on many variables. We began a meta-analysis of the publicly-available indoor biome data sets to compile and assess the state of current knowledge on the microbiology of the built environment. We hope to use the online QIIME database to analyze 16s and fungal clone data sets from multiple sequencing platforms. This kind of meta-analysis will hopefully help us to answer some of the following questions:

1. Are there consistent patterns for the processes (geography, building type, etc) structuring microbial communities indoors?

2. Can we identify consistent source habitats for different habitats in the BE?

3. Are there similar patterns between fungi and bacteria?

4. How does study design/sequencing method (e.g. clones vs. 454 vs. Illumina data) affect patterns?

5. Related to point 4, a meta-analysis will inform further studies’ experimental design, elucidating where/when/how we currently do not have any/few data (i.e. undeveloped nations, winter, rural communities, fungi in general).

We are hoping to undertake computational analysis in October, once all of our datasets have been put together!


AAAR Annual Conference in Portland


Ann Womack will be presenting on the BioBE Center’s recently published paper, “Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source”, at the American Association for Aerosol Research Annual Conference just up the road in lovely Portland, OR. Ann’s talk will be part of a special symposium on bioaerosols and is one of several presentations focusing on bioaerosols in the built environment.