IHBE meeting organizers did a fantastic job at facilitating a remote meeting with a dozen speakers across multiple time zones. This included creating formatted slide decks for speakers to populate, coordinating sections by colors and symbols and providing respective virtual backgrounds for section speakers to use, and use of breakout rooms for smaller discussion groups.
I presented “Framing the discussion of microorganisms as a facet of social equity in human health“, and you can find a recorded version of the presentation here. There are no closed captions, but you can read the audio as annotations here:
The concept of “microbes and social equity” is one I’ve been playing with for a little over a year, and has developed into a colloquium course at the University of Oregon in 2019, an essay in PLoS Biology in 2019, and a consortium of researchers participating in “microbes and social equity part 2”. The Part 2 group has been developing some exciting research events planned for later in 2020, and those details will be forthcoming!
A collaborative review article that I was last author on was listed in the top 10% most downloaded papers of 208/2019 in the journal Indoor Air! Even more impressive, this review was published August 20, 2019, and it was still in the top 10% spanning from January 2019 – December 2019!!
This paper stems from my work on the microbiology of the built environment at BioBE, and reviews the interaction between chemistry, microbiology, and health in the built environment. It was co-authored and led by undergraduate students I was mentoring at the time, as well as research associates and PIs from the BioBE lab, and a variety of fabulous collaborators!
In October 2017, Dr. Rich Corsi came to visit Oregon for two weeks during a sabbatical from the University of Texas, Austin. During his stay, Rich and I, and other BioBE/ESBL researchers chatted about doing a pilot study that would bring UT’s indoor chemistry work together with BioBE’s indoor microbial work.
Since we began our collaboration in the fall of 2017, only one of the research team is still in their original position (Jeff Kline at ESBL)! Rich Corsi, Ying Xu, and myself have all gone on to faculty positions elsewhere, graduate student Chenyang Bi defended and started a post-doc position, and the two undergrads working with me, Susie Nunez and Samantha Velazquez, graduated and went on to other things! Science collaborations work best when they can stand the test of time and geography. The benefit to everyone moving around is that you are able to hold collaboration meetings in new and exciting places each time.
In addition to the literature review we collaborated on, we eventually did get a research pilot running, and it has now been published in PeerJ!
Chenyang Bi 2,3, Jeff Kline 1,4, Susie Nunez1,
Richard Corsi 3,5, Ying Xu 3,6, Suzanne L. Ishaq1,7*
1 Biology and
the Built Environment Center, University
of Oregon, Eugene, OR, 97403
of Civil Environmental Engineering, Virginia Polytechnic Institute and State University,
Blacksburg, VA 24061 (current)
of Civil, Architectural and Environmental Engineering, University of Texas,
Austin, TX 78712
Studies and Buildings Laboratory, University of Oregon, Eugene, OR, 97403
Maseeh College of Engineering and Computer Science, Portland State University,
Portland, OR 97207 (current)
6 Department of Building Science, Tsinghua University,
100084, Beijing, P. R. China (current)
7 School of Food and Agriculture, University of Maine, Orono, ME 04469 (current)
phthalate (DEHP) is a plasticizer used in consumer products and building
materials, including polyvinyl chloride flooring material. DEHP adsorbs from
material and leaches into soil, water, or dust, and presents an exposure risk
to building occupants by inhalation, ingestion, or absorption. A number of bacterial isolates are
demonstrated to degrade DEHP in culture, but bacteria may be susceptible to it
as well, thus this study examined the relation of DEHP to bacterial communities
in dust. Polyvinyl chloride flooring was
seeded with homogenized house dust and incubated for up to 14 days, and
bacterial communities in dust were identified at days 1, 7, and 14 using the
V3-V4 regions of the bacterial 16S rRNA gene.
DEHP concentration in dust increased over time, as expected, and
bacterial richness and Shannon diversity were negatively correlated with DEHP
sequence variants of Bacillus, Corynebacterium jeddahense, Streptococcus, and Peptoniphilus were relatively more abundant at low concentrations
of DEHP, while some Sphingomonas, Chryseobacterium, and a member of the
Enterobacteriaceae family were relatively more abundant at higher
concentrations. The built environment is
known to host lower microbial diversity and biomass than natural environments,
and DEHP or other chemicals indoors may contribute to this paucity.
Suzanne L. Ishaq1,2*, Maurisa Rapp2,3, Risa Byerly2,3, Loretta S. McClellan2, Maya R. O’Boyle2, Anika Nykanen2, Patrick J. Fuller2,4, Calvin Aas2, Jude M. Stone2, Sean Killpatrick2,4, Manami M. Uptegrove2, Alex Vischer2, Hannah Wolf2, Fiona Smallman2, Houston Eymann2,5, Simon Narode2, Ellee Stapleton6, Camille C. Cioffi7, Hannah Tavalire8
Biology and the Built Environment Center, University of Oregon
Robert D. Clark Honors College, University of Oregon
Department of Human Physiology, University of Oregon
Charles H. Lundquist College of Business, University of Oregon
School of Journalism and Communication, University of Oregon
Department of Landscape Architecture, University of Oregon
Counseling Psychology and Human Services, College of Education, University of Oregon
Institute of Ecology and Evolution, University of Oregon
What do ‘microbes’
have to do with social equity? On the surface, very little. But these little
organisms are integral to our health, the health of our natural environment,
and even impact the ‘health’ of the environments we have built. Early life and
the maturation of the immune system, our diet and lifestyle, and the quality of
our surrounding environment can all impact our health. Similarly, the loss,
gain, and retention of microorganisms — namely their flow from humans to the
environment and back — can greatly impact our health and well-being. It is
well-known that inequalities in access to perinatal care, healthy foods and
fiber, a safe and clean home, and to the natural environment can create and
arise from social inequality. Here, we frame access to microorganisms as a
facet of public health, and argue that health inequality may be compounded by
inequitable microbial exposure.
In just a four-week course, I introduced 15 undergraduates from the University of Oregon Clark Honors College to microorganisms and the myriad ways in which we need them. More than that, we talked about how access to things, like nutritious foods (and especially fiber), pre- and postnatal health care, or greenspace and city parks, could influence the microbial exposures you would have over your lifetime. Inequalities in that access – such as only putting parks in wealthier neighborhoods – creates social inequity in resource distribution, but it also creates inequity in microbial exposure and the effect on your health.
By the end of the that four weeks, the students, several guest researchers, and myself condensed these discussions into a single paper (a mighty undertaking, indeed).
And now that I’ve found a preprint server that accepts reviews/commentaries, it’s available for preview! The paper is currently under review and will be open-access when eventually published.
During the course, a number of guest lecturers were kind enough to lend us their expertise and their perspective:
introduce students to basic concepts, laboratory techniques, historical background, terminology, and technology related to microbial ecology in or on mammals,
familiarize students with online resources, including sequence repositories, scientific databases, and analysis tools,
discuss how host-associated microbiomes are shaped by the anatomy and lifestyle of the host, and how the microbiome can reflect onto the health and performance of the host, and
review current literature on host-associated microbial ecology.
Keeping it fresh
While I’ve taught similar material at Montana State University, and have plenty of teaching experience from my graduate teaching assistant days at the University of Vermont, I’ve learned that each student population is different, with a unique core knowledge base and interests. Thus, I developed this course from scratch, and constantly revised it during the semester to adjust to the pace and learning style of my students. A draft syllabus, as well as an example of a student’s final project, can be found on my GitHub.
To improve engagement, I tried to make the course (which did not have a lab section) more interactive. I offered a tour of the molecular biology lab I work in, I brought agar plates to class so students could try culturing their own microbiota, and I dressed up like a dead cat.
These students were not science majors, and had had very little science since high school. Even if they had been science majors, I wanted to give a broader look at the field of science than just giving an overview of current knowledge. At the end of some lectures, I facilitated class discussions on various topics in science: the role of scientists in communicating science and whether we should report only or have an obligation to convince the public; elitism, recognition, and credit for intellectual property in a highly-collaborative working environment; the transfer of maternal microbiota and health status to offspring and how we approach prenatal care and parental leave; air quality (and air microbiota), residential zoning in urban areas, and income inequality; should we eat dirt?, etc. The students enthusiastically participated in class discussions, and — to my surprise — requested more (see below).
Phone a friend
I wanted to highlight current research in host-associated microbiomes, and hosted three mini-lectures from guest researchers; Deepika Sundarraman, a graduate students in UO physics, Dr. Candace Williams, a postdoctoral researcher who Skyped in from Vienna, and Dr. Edward Pajarillo, a postdoctoral researcher who Skyped in from Florida.
I really enjoyed teaching this group of students, and I got regular feedback from them about how the course was going and what was working. More formally, I volunteered the class to participate in a pilot evaluation for my midterm and end of term review, which asked more probing questions of students than typical teaching evaluations. For the midterm, only 4 of 15 students responded, but for the final, 13 of 15 responded and I have decided to share those (anonymous) course evaluations for IMM2018:
Students wanted more in-class discussions, and more group-based work, which was surprising to me as science students tend to prefer fewer of these, or at least the option to opt out. I am already considering additional topics for discussion next year. While there was an option on the final to submit a group project, no one chose to pursue that. Similarly, students were able to work collaboratively on journal article summaries to improve their comprehension, provided each student submitted a unique response. Perhaps this option simply needs to be reiterated.
What surprised me most about the evaluations was that several students replied that (the second half of) the course was not challenging enough. The course content was entirely new to them, and while the assignments drew on skills from their core competency as humanities students (reading and writing), they were required to distill large amounts of scientific information and be able to explain it back to me. It’s a challenge to serve the learning speed and style of all students in a class, and I try to manage this by varying the format of assignments, as well as to teach skills in the first part of the class which can be refined with successive assignments.
An example of this was the final project, for which the students needed to create a public outreach presentation in the format of their choice (essay, poster, pamphlet, presentation), which covered a particular topic or discussion point on host-associated microbial communities. Students were able to draw from scientific article summaries they had previously written, or even material from their exams (take-home essays), provided it was more developed and presented in a new and creative way. This flexibility allowed students to choose topics that they were passionate about, and to focus on the message rather the format. I felt this would help them find their voice, and judging by the final projects I received, it was effective.
That being said, if humanities students thought the material too easy, I take credit for communicating it well. I’m pleased with how the course turned out, as well as with the feedback I received from students. I’ve already begun implementing upgrades to my curricula, and have proposed this course again to the Honors College. Pending approval, I’ll be back at it next year!
Since the end of September, I’ve been teaching a course for the UO Clark Honors College; Introduction to Mammalian Microbiomes. And in a novel challenge for me – I’m teaching the idea of complex, dynamic microbial ecosystems and their interaction with animal hosts … to non-majors. My undergraduate students almost entirely hail from the humanities and liberal arts, and I couldn’t be more pleased. So far, it’s been a wonderful opportunity for me to pilot a newly developed course, improve my teaching skills, and flex my creativity, both in how I explain concepts and how I design course objectives.
Welcome to Introducion to Mammalian Microbiomes! I had a great first class and am enthusiastic about what we'll achieve this semester! pic.twitter.com/ejwoze7h3o
I enthusiastically support efforts towards science communication, especially in making science more accessible to a wider audience. My students likely won’t be scientific researchers themselves, but some will be reporting on science publications, or considering funding bills, and all of them are exposed to information about human-associated microbial communities from a variety of sources. To navigate the complicated and occasionally conflicting deluge of information online about the human microbiome, my students will need to build skills in scientific article reading comprehension, critical thinking, and discussion. To that end, many of my assignments are designed to engage students in these skills.
I feel that it’s important to teach not only what we know about the microbial community living in the mouth or the skin, but to teach the technologies that provide that knowledge, and how that technology has informed our working theories and understanding of microbiology over centuries. Importantly, I hope to teach them that science, and health sciences, are not static fields, we are learning new things every day. I don’t just teach about what science has done right, but I try to put our accomplishments in the context of the number of years and personnel to achieve publications, or the counter-theories that were posited and disproved along the way.
Today in #IntroMammalianMicrobiomes, I talk about DNA-based technology and Rosalind Franklin, while wearing a shirt with her face on it. This will be lost on my students, as I'm Skyping my lecture from home as I fight a cold, and playing the role of disembodied narrator. pic.twitter.com/K2LSZ97CXa
And most of, I want the course to be engaging, interesting, and thought provoking. I encouraged class discussions and student questions as they puzzle through complex theories, and I’ve included a few surprise additions to the syllabus along the way. Yesterday, University of Oregon physics Ph.D. student Deepika Sundarraman taught us about her research in Dr. Parthasarathy’s lab on using light sheet fluorescence microscopy to visualize bacterial communities in the digestive tract of larval zebra fish! Stay tuned for more fun in #IntroMammalianMicrobiomes!
The end of 2017 marks the second year of my website, as well as another year of life-changing events, and reflecting on the past year’s milestones help put all those long hours into perspective. I reviewed my year last year, and found it particularly helpful in focusing my goals for the year ahead.
This involved another large move, not only from Montana to Oregon, which has led to some awesome new adventures, but also from agriculture and animal science to indoor microbiomes and building science. So far, it has been a wonderful learning experience for incorporating research techniques and perspectives from other fields into my work.
This year, I added fournewresearchpublications and one review publication to my C.V., and received word that a massive collaborative study that I contributed to was accepted for publication- more on that once it’s available. In April, I hosted a day of workshops on soil microbes for the Expanding Your Horizons for Girls program at MSU, and I gave a seminar at UO on host-associated microbiomes while dressed up as a dissected cat on Halloween. In November, I participated in a Design Champs webinar; a pilot series from BioBE which provides informational discussions to small groups of building designers on aspects of how architecture and biology interact.
I published 34 posts in 2017, including this one, which is significantly fewer than the 45 I published in 2016. However, I have doubled my visitor traffic and views over last year’s totals: over 2,000 visitors with over 3,200 page views in 2017! My highest-traffic day was April 27th, 2017. While I am most popular in the United States, I have had visitors from 92 countries this year!
I also added some “life” to my work-life balance; in November, I married my best friend and “chief contributor“, Lee Warren, in a small, stress-free ceremony with some local friends in Eugene, Oregon!!
I have high hopes for 2018, notably, I’d like to finish more of the projects that have been in development over the last two years during my post-docs. Nearly all academics carry forward old projects: some need additional time for experimentation or writing, some get shelved temporarily due to funding or time constraints, some datasets get forgotten and gather dust, and some which got cut short because of the need to move to a new job. This is a particular concern as grant funding and length of job postings become shorter, forcing researchers to cut multi-year projects short or finish them on their own time. After defending in early 2015, I had two one-year postings and started at UO in June 2017, making this my fourth job in three years. I’m looking forward to roosting for a bit, not only to clear out unfinished business, but also to settle into my new job at BioBE. This fall, I have been analyzing data on a weatherization project, writing a handful of grants, and developing pilot projects with collaborators. I have really enjoyed my first six months at BioBE, and Lee and I have taken a shine to Eugene. In the next few months, I hope to have more posts about my work there, exciting new developments in BioBE and ESBL, and more insights into the work life of an academic. Happy New Year!
My first day started auspiciously as I charted a new bike route to work, about 4.5 mi of which is along a path snaking next to the Willamette River. It goes through several parks, and by a few small lakes and swamps which are home to dozens of species of birds, mammals, amphibians, and reptiles. I haven’t seen any river otters yet, but I have been keeping a close eye out.
Arriving on campus, most of my first day, and first week, were spent visiting the various places around campus to get myself established as a new employee- obtaining my ID card and email address, filing out paperwork, attending orientation, and finding all the coffee places within walking distance of the building. ESBL is renovating and expanding its offices across several large, pluripotent rooms to accommodate a growing research team, so I got a brand new standing desk, chair, shelving, and computers (on order), all to my specifications. The flexibility of working position, screen size, and screen angle provided by my new station are comfortable and great for productivity, and it’s neat to design the new space into offices, meeting tables, and storage which are based on our personalized usage needs and preferences. And of course, there is plenty of space for all the mementos and science toys I’ve accumulated.
Most importantly, my first week was spent acclimating to my new department and getting up to speed on the ongoing and planned projects. BioBE and ESBL have dozens on ongoing or planned projects on the built environment, with a combination of building and biology facets. Over the course of the summer, I’ll be writing several grants and organizing new projects that explore how building use, occupancy, and human habits affect human health and the indoor microbiome, as well as contributing to the BioBE blog, providing building microbiome posts to Give Me the Short Version, and getting some older projects out for publication. On top of that, I’m looking forward to exploring the Pacific coast and the Northwestern landscape, and availing myself of the Willamette Valley wine industry.