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:

Report from the Mycological Society

In July, one of our own, Dr. Roo Vandegrift, went to the annual Mycological Society of America (MSA) meeting, held just outside of Atlanta, Georgia, in the college town of Athens. He went to learn what others in the field are up to, and present work from the BioBE Center. Roo live-tweeted most of the talks he went to; you can find him @MycoRoo on twitter to look back through his experience of the conference, and look up the hashtag #MSA17 or #MSA2017 to see other posts about the conference.

The meeting started with a pre-conference foray: a group of nearly one hundred mycologists loaded into three packed busses and went out to Unicoi State Park for a 3.5 mile hike; collecting mushrooms, ascomycetes, and plant pathogenic fungi all the way. It has apparently been a particularly wet summer in Georgia so far, and the fungal diversity on display was astonishing, particularly coming from Oregon, where our summers are dry and a bit mycologically deprived.

On Monday morning, the day started with the Presidential Address from outgoing president, Dr. Georgiana May, titled “Lucky: A career in mycology.” She gave a rolling account of a career full of lucky breaks and fortuitous moments, which she made the best possible use of with her sharp and grateful mind. She also included a number of historical anecdotes that had the audience in stitches of laughter, and sometimes on the verge of tears. She asked that the contents of her talk remain private, though, so that’s as much detail as I’ll give here.

The first session of talks that I went to was the Ecology & Conservation section, which started with Terry Henkel presenting some amazing work from his lab on the Thelephoralean ectomycorrhizal fungi of a monodominant tropical forest in the Guyana shield region of South America, and how these fungi may be involved in seedling survival and recruitment in this forest. The discussion of this system continued with the next talk in the session, from Terry’s graduate student, Carolyn Delevich, who gave a fascinating discussion of the community assembly of ectomycorrhizal fungi on the roots of these dominant Fabaceae trees, looking at the change in the community over time on the seedlings from one of these mass fruiting events.

There were a number of other excellent talks about mycorrhizal communities, highlighting the cutting edge of molecular techniques in fungal community ecology, host-associated dynamics, and spatial/temporal ecology. Dr. Alija Mujic’s talk on invasion dynamics in mycorrhizal communities of Nothofagus in Patagonia was particularly good.

At the end of that first day, Roo presented his talk: “Impacts of Weatherization on Indoor Fungal Communities“, co-authored with other BioBE personnel, as well as colleagues from the Oregon Research Institute and Northwestern University (Roo Vandegrift, Ashkaan Fahimipour, Jeff Kline, Alejandro Manzo, Dale Northcutt, Jason Stenson, Hannah Wilson, Ryann Crowley, Erica Hartmann, Deborah Johnson-Shelton, G.Z. Brown, Jessica Green, Kevin Van Den Wymelenberg). This talk debuted preliminary data from our EPA-funded study examining a multi-faceted, interdisciplinary dataset combining microbial ecology, indoor air quality, and an extensive survey detailing aspects of health and behavior. Feedback was incredibly positive and encouraging, including some really helpful feedback on biophysical explanations for observed trends in the data.

There were a handful of other talks that stood out as particularly important or impactful. Mara DeMers, from the University of Minnesota, Twin Cities, presented on endophytic fungi in prairie plants, and whether molecular OTUs (or ESVs, for that matter) correspond to species; she asks the question does it matter if they do? She was particularly vexed by the genus Alternaria, which made up most of her endophyte sequences, and appears to be non-resolvable into meaningful groupings via ITS alone — the region is so variable in this group (and other!), that the intra-strain variation is as great as the inter-strain variation, meaning that the same sequence may belong to totally different strains, while very different sequences may belong to extremely closely related individuals. This is an important caution for the field, and one we at the BioBE Center will certainly keep in mind!

Among the amazing talks, excellent company, and stimulating scientific conversations, Dr. Regine Kahmann (from Max Planck Institute for Terrestrial Microbiology) presented the the Karling Lecture, titled “Core Effectors in Smut Fungi: An Amazing Treasure Box.” This was an incredible summary of her life’s work on the molecular mechanisms underlying the pathogenicity and ecology of smut fungi (Ustilagomycota). The careful, methodical, innovative science on display during her talk was breathtaking, and an inspiration.

One other talk strikes me as worth explicit mention here: Jesse Uehling’s discussion of how to re-purpose archived data in new ways. I think there’s an important lesson here; we are generating sequence data much more rapidly than we are currently exhausting the ways that such data can be explored, and the techniques for exploring that data are evolving extremely rapidly. As Jesse says, there may be treasure in that trash!

One idea from her talk that struck me as particularly significant was that the “junk” reads from genomic assemblies are typically reads representing the microbiome of whatever organism was sequenced. It is certainly worth considering that there may be a large quantity of un-examined microbiome data available from a wide range of organisms, if we only go looking through the available raw data. And, the assembly of small bacterial genomes from mixed starting templates has been well demonstrated.

There were many other noteworthy aspects to this meeting; it is worth browsing the #MSA17 tweets if you’re interested. We hope for many more productive, fascinating meetings like this in the future!

~~

Roo wore a different mushroom-patterned bowtie every day of the meeting. We’re not sure why he was so pleased about this.

BioBE and ESBL are seeking a new Office Manager!

BioBE and ESBL are looking to a hire an office manager to support our teams!  The full position description and application can be found here.

The position will serve as the primary business officer in charge of coordinating and supporting both labs’ fiscal and administrative operations. In this capacity, the OM assists the lab director, research faculty, research staff, and students in developing and executing annual operating plans, conducting budget forecasts, identifying and procuring grants and contracts, building budgets and scopes of work for proposals, managing allocations of space/equipment and staff resources, and participating in and developing sales and client relationships.

As such, we are looking for someone with excellent written and oral communication skills, who can dynamically interface between the biology and building design teams and our administrative needs.  We need someone who has experience in project management and budgeting, who can properly handle confidential information, and who can proactively engage with team members and clients to identify potential conflicts and solutions.  This position will require you to work independently, and may require occasional nights and/or weekends to fulfill special projects or events, as well as the timely interaction with clients.

Minimum Requirements
• Bachelor’s degree from accredited college or university.
• Five or more years of administrative experience, or relevant transferable experience.
• Experience managing a budget, or relevant transferable experience.
• Experience in a lead or supervisory role.

Preferred Qualifications
• Master’s degree or advanced degree in relevant field
• Research and/or grant management experience
• Demonstrated knowledge of regulatory issues related to sponsored projects and an ability to satisfy federal, state and university regulations, while advancing the goal of creating a facilitative environment for faculty research.
• Expertise with Banner and EPCS systems.