2017 AIA Design & Health Research Consortium Convening

On March 21-22, the BioBE Center team took to Detroit to present “Biology & Buildings: How Indoor Environments Affect Human Health” to the American Institute of Architects Design & Health Research Consortium.  We were encouraged to see the diversity of research blooming at our fellow ACSA schools of architecture. For example, Joseph Kennedy from the NewSchool of Architecture & Design presented fascinating work on natural building materials in a panel discussion with members of the BioBE team. Bita Kash from Texas A&M University presented excellent work on integrating health and design, discussing ideas of fundamental adjacencies in the design process. Every panel was excellent, and the broad concern for integration of empirical methods to design evaluation was wonderful to see.

Most interesting was to learn from leading architecture firms about how they integrate research into their design practices and how they have developed funding models to support this research.  Upali Nanda (@upalinanda) of HKS Architects (Houston) talked about the importance of pooling research resources and openly sharing new knowledge in order to more rapidly progress the field and avoid redundancy.  Jeri Brittin, Director of Research at HDR Architects (Omaha) eloquently described how the research design process shares similarities with the building design process and how she has effectively used this analogy to explain the value of a rigorous research design process to firm decision makers.  Robert Phinney (@rsphinney), Sustainable Design Director at Page Architects (Washington DC), described the uphill climb that many firms face when trying to meaningfully integrate original research into the building design practice, stressing that measurable outcomes and financial metrics dominate the discourse.  What was most encouraging was that all three firm leaders described the immense value to their firms and clients of maintaining a tight relationship with university research and how rewarding it can be to work with academics to leverage their technical skills to help overcome the “pain points” facing their practice.  We couldn’t agree more!

Some of our most rewarding research has been closely linked with practical industry needs. However, there are some challenges that we face in the academy when integrating our work with industry objective.  First and foremost, is to ensure academic integrity when creating the research design to avoid real or perceived biases associated with industry engaged research.  Without this, the research has no value to industry or to science.  Other important considerations is to be nimble enough to complete the research at the “speed of business” and to work out possible concerns with intellectual property.  All of these, and other concerns, can be, and have been overcome.  The result in an opportunity to bring the leading scientific processes and utmost rigor to important problems that face society.  Industry partners can help to focus academic research and help it gain traction to make greater impact more rapidly.  It is for these reasons that we have launched a new industry engagement model here at the University of Oregon.

Mhuireach Awarded A&AA Dissertation Fellowship 2017-2018

Congratulations to Gwynne Mhuireach for winning a Dissertation Fellowship from the School of Architecture & Allied Arts at the University of Oregon!  Her working dissertation title is: Toward a Mechanistic Understanding of Relationships Between Airborne Microbial Communities and Urban Vegetation: Implications for Urban Planning and Human Well-being.  Mhuireach holds an M.Architecture (2012) from the University of Oregon and a B.S. in Biology (Ecology and Evolution Track, 1999) form the University of Washington. She is presently a Graduate Research Fellow at the Energy Studies in Buildings Laboratory and BioBE Center at University of Oregon.  Her anticipated graduation is June 2018.

Recent publication: Urban greenness influences airborne bacterial community composition

Dissertation Abstract: Variation in exposure to environmental microbial communities has been implicated in the etiology of allergies, asthma and other immune-related disorders. In particular, exposure to a high diversity of microbes during early life, for example through living in highly vegetated environments like farms or forests, may have specific health benefits, including immune system development and stimulation. In the face of rapidly growing cities and potential reductions in urban green space, it is vital to clarify whether and how microbial community composition is related to vegetation. The purpose of my proposed research is to identify plausible but under-explored mechanisms through which urban vegetation may influence public health. Specifically, I am investigating how airborne microbial communities vary with the amount, structural diversity, and/or species composition of green space for 50 sites in Eugene, Oregon. My approach combines geographic information systems (GIS) and remote sensing data with passive air sampling and culture-independent microbial sequencing.

Committee members:

  • Dr. Bart Johnson, Professor of Landscape Architecture (Major Advisor & Committee Chair)
  • Dr. Jessica Green, Professor of Biology (Co-Advisor)
  • Roxi Thoren, Associate Professor of Landscape Architecture (Core Member)
  • Dr. Deb Johnson-Shelton, Education/Health Researcher, Oregon Research Institute (Core Member)
  • G.Z. Brown, Professor of Architecture (Institutional Representative)




Health + Energy Research Consortium

The Biology and the Built Environment Center (BioBE) and Energy Studies in Buildings Laboratory (ESBL) at the University of Oregon, are pleased to announce the launch of the the Health + Energy Research Consortium!  On May 4-5, 2017, in Portland Oregon, we begin our journey to dramatically reduce energy consumption and maximize human health by conducting research that transforms the design, construction and operation of built environments. This collaboration between innovative industry professionals and academic researchers in the disciplines of architecture, biology, chemistry, engineering, and urban design provides sharp focus to a research agenda that will accelerate the impact of key scientific discoveries.  The Health + Energy Research Consortium builds upon the momentum of ESBL and BioBE to create a new, dynamic, and flexible mechanism for the university to engage with industry in joint research and development ventures – providing intellectual space for the meeting of a wide array of disciplines that play integral roles in fostering improved energy efficiency and health outcomes in the built environment.

At the May 4-5 launch event , we will present the vision for the Consortium, solicit feedback about the proposed research agenda, explain and discuss the financial commitments and value proposition associated with Consortium membership, and discuss synergies with potential member organizations’ goals and objectives.  If you are interested in helping us align the Consortium research vision with the challenges that face our built environment and your industry sector, please contact BioBE Director, Kevin Van Den Wymelenberg.

We would like to acknowledge the generous support for the Health + Energy Research Consortium from the Alfred P. Sloan Foundation.  Registration is required, but the event is available at no charge.

EPA Progress Meeting

Jeff Kline presented BioBE’s project, “The Impact of Weatherization on Microbial Ecology and Human Health” at EPA’s Science to Achieve Results (STAR) Indoor Air & Climate Change Progress Review Meeting and Webinar.  The meeting was held in December in Washington, D.C. The presentations will be made available on the meeting website.



Multiple Positions Open at University of Oregon BioBE Center

Kevin Van Den Wymelenberg and Jessica Green, of the Biology and the Built Environment Center (BioBE), are currently seeking a microbial ecology Research Associate / Research Assistant Professor / Research Associate Professor (non-tenure track faculty) to investigate fundamental questions surrounding the role of microorganisms (bacteria, archaea, fungi, protists, and viruses) in the built environment and in relation to human health outcomes. Applicants must have a Ph.D. in biology, bioinformatics, or a related discipline.

The ideal candidate will have a combination of domain expertise and leadership potential. With regards to domain expertise, candidates should possess a demonstrated ability to generate and interpret microbiome data. Deep knowledge in data analytics, bioinformatics, and/or clinical microbiology is highly desirable. From a leadership perspective, we are seeking candidates that: are comfortable working on multiple concurrent projects with interdisciplinary scientists comprising a diverse range of experience (undergraduate through postdoc); have demonstrated a record of scientific writing and scholarly productivity; have a record of, or evidence of potential for, obtaining external research funding.

The successful candidate will have the ability to work with faculty, students, and industry partners from a variety of diverse backgrounds and the opportunity to creatively and independently engage in research at the BioBE Center (http://biobe.uoregon.edu/), funded by the Alfred P. Sloan Foundation, federal agencies, and members of industry.

The BioBE Center is training a new generation of innovators to study the built environment microbiome, including the diversity of microorganisms interacting with each other and with the indoor environment. The vision of this national research center is to understand buildings and urban environments as complex systems and to explore how urban, architectural, and building system (passive and active) design work to shape the microbiome, with the ultimate goal of designing healthy and sustainable buildings and cities.

For more information or to apply, see the full job post.

The concept of hygiene and the human microbiome.

Reblogged from MicrobeBE.net.

(This post was written by Roo Vandegrift, at the University of Oregon)

I was recently asked to spearhead the writing of a review centered around the interaction between the concept of hygiene and our increasingly nuanced understanding of the human skin microbiome for the Biology and the Built Environment (BioBE) Center at the University of Oregon.

This review began with an invitation from Dyson to conduct an impartial review of hand drying studies, which have been mired in competing interests and faulty methods. We saw an opportunity to not only provide an unbiased review of the literature, but also to ask a more fundamental question: how should hygiene be defined in light of our evolving perspective of the human and indoor microbiome?  We delivered a brief summary to Dyson (here) and then built upon that work to develop this question.  

As we started digging into the body of literature on hand hygiene, two things struck us as peculiar: the first was that in the hundreds of studies explicitly examining hygiene, the concept was never explicitly defined; the second was that there seemed to be a clear division between skin microbiological investigations coming from clinically and ecologically informed perspectives, with clinical research generally relying on older cultivation-dependent techniques. These two issues became the drivers for our review, and our goal was to provide an explicit definition of hygiene that would help to bridge the gap between the clinical skin microbiology literature and the newer human-associated microbial ecology literature. We were then able to use the body of literature on hand drying as a case-study to examine the implications of using a microbial ecology-based approach to defining hygiene.

You can read the full review as a preprint on bioRxiv now: http://biorxiv.org/content/early/2016/12/20/0957450

You can read the shorter, white page summary of the review on the BioBE blog: https://biobe.uoregon.edu/2016/11/04/cleanliness-in-context

Continue reading

Cleanliness in Context


The BioBE Center just published a white paper, titled “Hand Hygiene in the 21st Century: Cleanliness in Context” that examines the history and current literature on hygiene. Specifically, the paper focuses on the role of hand drying and the debate in the literature surrounding paper towels and electric hand dryers. We posit that the conception of hygiene as a unilateral reduction or removal of microorganisms has outlived its usefulness, and propose a definition that is quantitative, uses modern molecular biology tools, and is focused on disease reduction.  20170102_BioBE_Hygiene_Dyson_summary

Edit 2017.01.11: updated white paper to reflect most recent version, added image.

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!