Twelve Days at the University of Oregon

Written by Dr. Rich Corsi, edited by Sue Ishaq and Jeff Kline.

Several months ago, I connected with Dr. Kevin van Den Wymelenberg at the University of Oregon about the interaction between indoor microbiology and indoor chemistry, and several other common interests.  We also discussed the possibility of having me visit the University of Oregon during my fall semester leave from the University of Texas at Austin.  I visited the University of Oregon for 12 days in October, and I am so glad that I did.

Kevin walks in fairly large circles while wearing a lot of hats at the University of Oregon.  He is the Director of the Energy Studies in Buildings Laboratory (ESBL), and Co-director of the Biology of the Built Environment (BioBE) center, and this summer and fall has been serving as the interim Head of the Department of Architecture. The BioBE center is a unique initiative funded by the Alfred P. Sloan Foundation’s Microbiology of the Built Environment (MoBE) program.  Prior to my visit I was already aware of, and impressed by, how BioBE has effectively built a community of scholars that bridge two disparate disciplines; architecture and microbiology, in a transdisciplinary manner.  That impression was underscored and reinforced during my visit.

Me, Kevin, and Sue in front of our artistic interpretation of our research!

I delivered two seminars during my visit, both in the School of Architecture and both entitled Living in a Material World – How the Surfaces that Surround You Affect What You Breathe.  One of these was delivered on the main campus of the University of Oregon in Eugene, and the other to the School of Architecture’s program in Portland.  The latter also contains the ESBL’s climate chamber facility, which is a highly-controlled and impressive instrument for studying indoor environmental quality.  The seminars were well attended, and the questions and discussion which followed each were both insightful and creative.

I also interacted with numerous individuals during my visit, most of whom are dedicated to improvements in building energy consumption, as well as expanding knowledge related to indoor air quality and particularly microbiomes of buildings. We discussed their ongoing projects, including one involving the effects of lighting on bacteria in residential dust and funded by the Alfred P. Sloan Foundation (Link: ) and another on  home weatherization funded by  the U.S. EPA.  This led to a broader discussion about future research with BioBE’s Sue Ishaq and ESBL’s Jeff Kline, about the impacts that home weatherization and operation, as well as human behavior can have on indoor chemistry, for example, the use of air fresheners or cooking, which release highly reactive unsaturated organic gases and particles to indoor environments.  We even wondered whether indoor chemistry would impact microbial communities, and our discussions sparked a few pilot projects between myself, BioBE/ESBL, and one of my colleagues at the University of Texas at Austin.

There were many other great interactions during my visit to the University of Oregon, including one with Isabel Rivera, a Ph.D. student who is doing important work on indoor air quality and thermal comfort in elementary school classrooms in Chile.  I conveyed to Isabel some of the findings from my own studies on indoor air quality in schools in Texas, as well as ideas for low-cost measurements of pollutants emitted from unvented space heaters in Chilean schools.

Not all of the time during my visit was for work.  Eugene is a great city for walking.  The weather was fantastic and fall colors were in the height of their flare.  I walked everywhere.  I walked and walked and walked, then rested a bit and walked some more.  A highlight was visiting the historic Mims home near downtown Eugene.

 

Another highlight was attending an Oregon Ducks football game (they beat the Utes).  My ex-PhD student, Elliott Gall, now an assistant professor at Portland State University, came down to Eugene for the game.  Great fun – and I have learned to appreciate both the quack attack and the hand gesture “O” (for University of Oregon). All in all, I was impressed by everything Eugene, at the center of which was the University of Oregon and the people at ESBL and BioBE.

Go Ducks!

Design Champs: Daylight and Microbes

This week, BioBE held the third session of our “Design Champions” webinar series, which we have been developing over the last few months as a means of actively communicating our work with industry professionals.  Design Champs brings together a small number of industry participants, to better facilitate a targeted discussion on topics relevant to building design, energy, and health in the built environment.  Design Champs is a great way for us to summarize the current body of research on a particular topic, present our work, and brainstorm with industry professionals about what next steps we need to take to fill knowledge gaps.  This week, Jeff Kline, Ashkaan Fahimipour, Mark Fretz (our new Outreach Director), and myself (Sue Ishaq) connected online with a handful of architects from Oregon, Washington, and California to talk about “Daylight and Microbes”.

Mark presented a historical perspective on the use of light in architecture, and how factors like the price of glass shape the way buildings were and are designed, and even impact human health.

I added an overview of selected research into the effect that light has on bacteria, and how early results narrowed the focus of work into using light, particularly ultraviolet light, as a bactericidal treatment.  Yet, research has also found that other wavelengths affect bacteria in beneficial and detrimental ways, that other factors (like the presence of oxygen) can influence how dramatic that effect is, and how complex communities of microorganisms react differently than monocultures.

Next, Jeff presented a slide deck to illustrate the technical aspects of the work that BioBE has been doing to research light and microbes, including the design and creation of “lightboxes”.  This set up the last section for Ashkaan, who presented some of the results from our project studying different lighting regimes on the bacterial community in dust.  The manuscript from this project is currently in review, but we’ll be presenting on it more thoroughly once published.

BioBE is still developing the format for Design Champs, but we hope to host them every few months.  If you’d like to learn more, please email Jeff (jkline@uoregon.edu) or myself (sueishaq@uoregon.edu)!

ESBL/BioBE welcomes new Associate Director of Outreach

ESBL and BioBE are thrilled to announce that Mark Fretz has joined the team as the new Associate Director of Outreach, based out of the Portland location.  Mark brings a unique combination of experience in architecture and public health service, and will help further our goal of promoting health in the built environment through research, outreach, and knowledge exchange.

Mark has a history of successful collaboration with the lab- several years ago he was a research assistant with ESBL.  He helped to develop the idea and grant for our ongoing project on the effect of weatherization on indoor air quality, human health, and the indoor microbiome.  He was also involved developing field materials and pilot studies for our study on the effect of daylight on dust communities, currently in review.

Mark helping set up data collection boxes for the home weatherization project.
Installing “lightboxes” onto the roof of Pacific Hall for a bacterial community study.

In addition to developing future research, and teaching, Mark will primarily be developing the Institute for Health & the Built Environment consortium that ESBL and BioBE initiated in May 2017 with their inaugural meeting.  The Consortium aims to dramatically reduce energy consumption and maximize human health by conducting research that transforms the design, construction and operation of built environments. Mark will help foster collaboration between innovative industry professionals and academic researchers in the disciplines of architecture, biology, chemistry, engineering, and urban design,  provide sharp focus to our research agenda, and accelerate the impact of our scientific discoveries.

Welcome to the team!

National Academies of Science MoBE meeting

In mid-October, The Alfred P. Sloan Foundation and The National Academies of Sciences, Engineering and Medicine co-hosted the MoBE 2017 (Microbiology of the Built Environment) Research and Applications Symposium, in Washington, D.C.  The meeting brings together researchers, industry professionals, and funders to discuss the state of MoBE research and how to bridge the gap between research and application.  Some of the opening remarks to the meeting were given by Paula Olsiewki, Program Director at the Alfred P. Sloan Foundation, who gave a retrospective on the history of MoBE and the process of growing research fields.

A number of BioBE members and collaborators were in attendance and gave presentations, including Jess Green, Co-Director of BioBE, who gave a brief history on the research of BioBE, followed by more detailed narratives on how ventilation and bioaerosols, daylighting, and antimicrobial compounds are driving community structure of the indoor microbiome.  Jonathan Eisen, Professor at the University of California, Davis, gave some background on microBEnet and the massive effort to promote microbiology on social media and in education to give our work as much impact as possible.  Richard Corsi, Professor at the University of Texas, Austin, who just spent two weeks visiting BioBE, spoke about indoor chemistry and how building design, materials, and the indoor microbiome can all affect the types and concentrations of chemicals indoor- often to the detriment of our health.  Kent Duffy, architect at SRG, spoke about how microbial research has impacted architectural design, and how this information can be used to change the way we design spaces.

In addition to presentations on their recent work, a number of meeting participants also sat on several panels to discuss broader issues.  For example, “The Myth and Reality of MoBE Manipulation” panel, moderated by Rob Knight, University of California San Diego and featuring Rita Colwell, Jeffrey Siegel, Ilana Brito, and Jessica Green as panelists, discussed the challenges to improving MoBE research and outreach.  The panel discussed the need for more basic science and evidence-based applied studies, in order to make more informed decisions on when and how to make interventions.

The full list of speaker and panel videos can be found on the microBE.net YouTube Channel, the presentation slides can be found here, and photos here.

Alfred P. Sloan Foundation renews BioBE funding!

Dr. Van Den Wymelenberg, Biology and the Built Environment Center PI and Co-Director, is excited to announce that the Center has secured another two years of funding from The Alfred P. Sloan Foundation and their Microbiology of the Built Environment (MoBE) program.  Van Den Wymelenberg stated, “we are honored to have been awarded a final BioBE Center renewal.  This investment will help us transition to an alternate funding model that aims to progress this important field through both basic science and applied research.  The BioBE Center’s vision is to conduct research and apply this new MoBE knowledge in ways that will optimize the design and operation of buildings and public spaces to promote both human health and environmental sustainability.”

In 2010, The BioBE center was formally implemented with funding from the Sloan Foundation MoBE program.  The Sloan Foundation vision was that we would establish a multidisciplinary center to conduct innovative research on the built environment, while training early-career scientists, and promote the importance of this field to improve the quality of life for people.  For seven years, BioBE has brought together architects, microbiologists, ecologists, snd other researchers at the University of Oregon and a number of collaborating institutions. The Center was launched by Dr. Jessica Green, Dr. Brendan Bohanan, and Professor G.Z. “Charlie Brown”.  Co-PIs at the Center have included Dr. Rolf Halden at Arizona State University, Dr. Erica Hartmann at Northwestern University, and Dr. Curtis Huttenhower at the Harvard T. H. Chan School of Public Health.  The Center has also collaborated with Dr. Jonathan Eisen of UC-Davis in support of public outreach through microBE.net.

Previous BioBE awards have produced 16 peer-reviewed journal publications, over 80 conference and media outlet presentations, and trained over 20 researchers.  In May 2017, BioBE helped to launch the Institute for Health & the Built Environment and a knowledge-exchange industry/research consortium. We will be holding Consortium meetings at least annually, with the next meeting planned for early 2018.  Going forward,  we’ll be furthering our collaboration with the Eisen Lab to develop a sustainable outreach platform, building on microBE.net, and anticipate teaching a joint seminar series in which both architecture and biology faculty present.

With this Sloan funding renewal, we plan to progress the basic scientific research which has helped elucidate the ecological dynamics of microorganisms in the built environment, that will be the foundation for applied scientific research moving forward. Over the next two years, we will be conducting several projects to test, among other things, the effect of air, light, humidity, and materials on the indoor microbiome. We are currently building Scalar Airflow Microcosms to determine whether microbial communities will assemble in dust differently when  air from different microbial colonization sources (outdoors, indoors, or both) is provided to sterilized dust under different humidity levels. Similarly, we will be utilizing existing scalar “lightboxes” to quantify the changes in microbial community structure and viability over time in response to diurnal cycles of solar radiation exposure under different conditions.

We also have a project underway conducting room scale materials tests (wood, painted drywall, glass/concrete, strawbale) in our “climate chamber” to improve our understanding of the role that building materials have on microbial community structure, assembly, and functional profiles. Beginning with microbial community mapping of indoor spaces under different conditions, we are also developing mathematical models of indoor microbiome dynamics to characterize how spatial properties of real buildings relate to microbial population dynamics.

OCCRI Mini-Conference

We attended the Oregon Climate Change Research Institute Mini-Conference at Oregon State University on 10/18/17. This half-day event featured 4 minute lightning talks on a broad gamut of climate change related topics, including presentations on atmospheric modeling, meteorology, ocean and tidal science, vegetation impacts, public health, and legal efforts, and featuring an extended “conversation” on ethical and moral issues. Jeff Kline of BioBE presented a short talk titled “Consuming and Producing Climate change Research” which covered the building science and microbial ecology aspects of our work.

Combining multiple sequencing runs: heterogeneity spacers

We do a lot of Illumina-based metabarcode sequencing here at the BioBE center. Sequencing is getting cheaper, and the amount of data you can get from a sequencing run continues to increase, but not at the same rate: it is now becoming more and more common to sequence samples across multiple sequencing runs, because a single run does not provide the necessary sequencing depth.

The field, as a whole, is still trying to work out how combine samples from different sequencing runs: because the error rates and read distributions tend to be specific to a given sequencing run, it can be difficult to distinguish between run effects and biological effects.

We’ve recently run across an interesting case, while working to improve our bioinformatics pipelines.

It is common for sequencing facilities to spike in Phi-X DNA to add heterogeneity to the library being sequenced; this heterogeneity prevents synchronous fluorescence from any given base overwhelming the sensor (Phi-X reads are removed bioinformatically, generally by the sequencing facility). There is, however, a more sequencing-efficient way to introduce heterogeneity into your library: variable length spaces between the Illumina adapter and the target sequence. This method doesn’t “waste” sequencing on Phi-X, but still handily prevents synchronous fluorescence. The problem is, sometimes those spaces may not be fully removed before data processing.

In collaborating with colleagues to test various options for merging data from distinct sequencing runs, we were working with some problematic data that included samples re-sequenced in two different Illumina MiSeq runs. We discovered that they had such heterogeneity spaces that had not been removed by the sequencing facility. This didn’t matter at all when processing with QIIME and uclust, because the 97% OTU radius was enough to “lump” all of the spacer sequences into the same OTU, but when working with denoising tools that infer exact sequence variants (ESVs), like DADA2, it altered the ability to recognize that the dominant sequences from the same sample in the two different runs were the same.

Alignment showing heterogeneity spacers, and the artificial variation which that the may introduce.

There are several potential solutions to this problem, but the best one is to always make sure you understand your data fully, and remove any potential sources of artificial variation before inferring sequence variants or picking OTUs. Usually, that means searching for and removing the PCR primers from each sequence, along with any sequence behind them — there are many programs out there with this functionality, including the FastX toolkit, trimmomatic, and cutadapt. If you’re sequencing a variable length region, like the internal transcribed spacer (ITS) of the ribosomal DNA, this also has the benefit of removing artificial variation introduced by sequencing past the primer on the other side of the short amplicons.

Another potential solution if you’re using DADA2 is to use “100%” OTU clustering (that is collapsing all sequences that differ only be length into the same inferred variant). There is, conveniently, an option baked into dada() for that: collapseNoMismatch = TRUE. The DADA2 pipeline also did a much better job of recognizing that different sequences with artificial variation were actually the same when using pool = TRUE, although pooling all samples for sequence inference is likely too computationally intensive to be a viable solution.

Additionally, Paul McMurdie points out that we can look for irregularities early on with DADA2:

Another way to note this early in your process is to check that the error rates look reasonable for your platform/amplicon, e.g. if you had previous successful runs for that amplicon and seq platform, you could check that the error profiles are not wildly different. If they are, you usually have a problem with trimming.

I am, however, not able to see a clear signal of the heterogeneity spacers in the error profiles for this data. It may vary with the length and variation within the spacers — I’ll surely be adding an error profile check to my standard workflow, though.

After removing the primers and spaces, we get much better agreement between sequencing runs (although we still get 45–65% of ESVs in only one run or the other). We’re still investigating this particular issue: you can follow the ongoing discussion (and contribute!) on the DADA2 GitHub page.

 

Design Champs

Last week, the staff of the Biology and the Built Environment Center presented cutting-edge science from the Center and beyond to a group of interested practitioners. The Design Champs webinar series is intended to communicate new scientific advances in the field of indoor microbial ecology research to architects, engineers, and other interested parties. For this second seminar in the series, we had representatives in attendance from:

  • ZGF Architects
  • HOK
  • Thornton Tomasetti
  • SRG Partnership
  • Hacker Architects

The group was lively, and participated in a active discussion of some of the science we’ve been doing at the BioBE Center lately. In particular, we briefed them on some thoughts on hygiene that we’ve been having lately, and then discussed how that might impact the way we think about design; next, we discussed the human microbial cloud, tying the idea into the discussion of hygiene and design; this led smoothly to a discussion of some of our most recent work, focusing on the transmission of microbes to the human skin microbiome. After discussing how hygiene serves as a conceptual frame for understanding both of those studies, we went on to talk about antimicrobial compounds in built environments, and how that relates to the spread of antibiotic resistance genes.

The webinar finished with a preview of related new work — a much larger study on antibiotic resistance genes in indoor microbiota, conducted across dozen of gyms in the Pacific Northwest, and including the synergistic use of next-generation sequencing for metabarcoding and metagenomics, and targeted LC-MS/MS and intensive antibiotic-resistance culture assays in association with colleagues at Northwestern in Chicago.

So long, summer!

Written by Hannah Wilson

The beginning of my summer was dedicated to moving the BioBE center’s molecular biology lab to a new location on campus.

Sue, Roo, Ashkaan, and Jeff all pitched in the help pack up the old lab!
The lab is unpacked and up and running!

I dedicated the next part of my summer to finishing the DNA extractions for ~350 swab samples collected from cohort 2 of the EPA weatherization project, and then the corresponding fungal (ITS) and bacterial (16S) library prep (nearly 700 samples in the end). I also completed the DNA extractions and metagenomics library prep for the vacuumed dust samples of the EPA weatherization project (~150 samples), the DNA extractions and 16S library prep for Gwynne’s latest Urban Air data collection effort (~60 samples), as well as finishing the library prep for the adoption study that Ashley had been overseeing (~96 samples).  

In August I took some vacation time to visit Europe, traveling with my partner, Craig. We spent the first part of our trip in the French countryside. We got to go cheese tasting in medieval villages, and visit local markets, castles, and beautiful cathedrals.

We then traveled to the south of France, to Marseille and Toulon, and took a ferry to Sardinia. Sardinia was a very interesting place full of  rich history, culture, and amazing landscapes. 

We topped off our trip with a quick stopover in Amsterdam, where we had a lovely visit with Craig’s friends that he hadn’t seen since college.I spent the last part of the summer updating protocols, troubleshooting methods, working on manuscripts, and harvesting vegetables from my garden and making tomato sauce.

I’ve also been training a new addition to the lab, Mitch Rezzonico, who just started his Masters in Bioinformatics here at UO.  Mitch has been learning common lab techniques, like DNA extraction and PCR amplification, as well as helping Sue with some data analysis.

Mitch preparing for PCR.

Round up of ESA conference

The 2017 ESA meeting in Portland, OR, which took place August 6-11, created a flurry of imagination here in Eugene: Roo Vandegrift left with a large hash of approximately 275 live-tweets, Sue Ishaq left with a jumbled pile of hastily scribbled notes in the program book margins, a few of which she has expanded upon, and Ashkaan Fahimipour went away with the inscrutable expression of a mathematical modeler visualizing complex networks in their head. All three presented some of their recent or ongoing work, along with a number of other BioBE members and friends from the UO Institute of Evolution and Ecology.

The meeting started out with a number of engaging science activities, including the Field-to-Collection BioBlitz, which brought conference participants to Forest Park in Portland to collect biological samples for identification and curation. Forest Park is the largest urban forest in the United States, and the biological specimens collected will shed light on the number and types of diversity found there, as well as indicate the success of urban forests at harboring a sustainable level of biodiversity.

The plenary speech was given on Sunday evening, officially opening the conference, and presentations kicked off bright and early on Monday morning. Of the BioBE team, Roo was first to give a presentation on Monday afternoon, on a project led by the recently-defended Dr. Ashley Bateman for her dissertation: Moving Microbes: the dynamics of the skin microbiome in response to environmental exposures. (Revised; listed as “The built environment as a reservoir for transmission and colonization of the skin microbiome.”)

 

 

Erica Hartmann, Assistant Professor at Northwestern University, presented on Tuesday with a compelling talk on the importance of limiting antimicrobial chemicals in synthesized products: Antibiotic resistance and antimicrobial chemicals in the built environment. Antimicrobial chemicals are pervasive in the built and outdoor environments, much more than we realize, yet we have little knowledge of their long-term effect on microorganisms or how this might feed-back onto human health. The full publication can be found here.

Gwynne having a delightful time at her poster.

On Tuesday evening, doctoral candidate Gwynne Mhuireach presented her poster on Fine-scale urban vegetation patterns shape airborne microbial community composition.

Wednesday evening, Sue presented some preliminary data on a project she is finishing up from her post-doc: Soil bacterial diversity in response to stress from farming system, climate change, weed diversity, and wheat streak virus (poster). A more detailed description of her previous work can be found here.

Ashkaan gave a presentation on Thursday on The dynamics of food web assembly: Structure, stability, and trophic cascades.  The study explored how empty ecosystems acquire new species, how the food web develops over time, and how the trophic niches of those colonists can determine the total diversity of the ecosystem or weather disturbances. The large meeting room was well-attended, despite the low total abundance pictured- ecologists don’t seem to like to sit in the front rows.

 

In between our presentations, we filled our days by attending other talks and posters, networking events, and daydreaming about our own science.  We took away valuable perspectives on newly discovered results, considerations for data analysis, or the dynamics of ecological systems, which can be incorporated into our own work to improve how we think about indoor systems and approach problem solving.  You never know when a presentation on shower heads, baboons, or dormant amoeba might give you an idea which will change the way you think.

Looking ahead, we are anticipating attending a number of conferences on microbiology, air quality, building health, architecture, and ecology over the next year. Here are a few of the meetings that are already on our calendars: