“Microbes and social equity”: I’m teaching a new UO Honors College summer course!

I’ll be teaching a new course for the UO Clark Honor’s College this summer!

Course Description: Microbes and social equity

This colloquium course introduces students to current knowledge on selected host-associated or human-associated microbiomes, and uses that base knowledge to discuss their relevance to human health in the context of social equity.  Example topics include the effect of diet on the microbial community in the gut and the importance of nutrient composition of free school lunches; maternal stress and the effect on offspring physiology, immune development, and host-microbial interactions; microbial communities in air, air quality, and income-based housing; building quality, indoor microbiology, and enforced occupancy (ex. prisons or public schools); and more. Guest lectures from relevant experts will be included as possible.

Some background in microbial ecology, genetics, anatomy, immunology, or sociology would be helpful, but is not required.  While difficult concepts will be discussed, the course is intended to teach students about the basic principles and how to apply them to contemporary social issues: what is a microbiome? How does host anatomy and health drive microbial ecology?  How does environmental microbiology and building microbiology contribute to or impinge on health? When we read about host-associated microbiomes in the news, especially regarding health, how can we assess if the study is rigorous and how should we interpret the scope of the findings?  The skill-set objectives include learning to review scientific journal articles, distilling their findings while understanding their limitations, and developing science communication skills via written assignments and in-class discussions.

Lessons learned: a retrospective on a newly developed course

This fall, I developed and taught a course called Introduction to Mammalian Microbiomes for the University of Oregon Clark Honors College.  The course objectives were to:

  1. introduce students to basic concepts, laboratory techniques, historical background, terminology, and technology related to microbial ecology in or on mammals,
  2. familiarize students with online resources, including sequence repositories, scientific databases, and analysis tools,
  3. 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
  4. review current literature on host-associated microbial ecology.
As always, include plenty of humor.

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!

Introduction to Mammalian Microbiomes

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.

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.

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!


Spring Updates

It’s been a really busy spring so far, so much so that I haven’t had much chance to write about it!  Here is a brief overview of what I’ve been up to.


This past year has easily produced the largest number of research topics I have been working on concurrently.  In addition to publishing a paper on the rumen in cattle last September, I have been working on a paper on the rumen of yearling rams which is currently in preparation and due to be submitted to a scientific journal for review soon.  I still have several small projects in development from my post-doc in the Yeoman lab, as well as a number of grad-student-led papers that are still pending, and was invited to contribute to a scientific review which is also in preparation.

I’ve been working through the large dataset of soil samples from my post-doc in the Menalled lab.  That large project has blossomed into four papers thus far, two of which I’m writing on the soil bacteria, and one of which I am co-authoring on the legacy effects of climate change.  Those four are also due for submission to scientific journals for review soon.  The Menalled lab just received a grant award from USDA AFRI NIFA, on which I am a (subaward) PI and to which I will be contributing soil bacterial community analysis.

The rumen and soil work over the past year has been entirely in my spare time, however, as my position in the Biology and the Built Environment Center has kept me delightful busy.  I have been collaboratively processing a large and complex dataset on weatherization, home operation and lifestyle, indoor air quality, and microorganisms in dust, which I will be presenting at two (possibly three) conferences this summer.  I have also been collaboratively writing grant proposals, and while those are still in development or pending review, they span everything from light, to chemistry, to plants and living machines, to hospitals, to social networks in buildings.  I hope to further develop some of these collaborations with a short trip at the end of June to the University of Austin, Texas’ Test House.

In addition, I have been assisting in the planning, development, and launch of the University of Oregon’s Institute for Health in the Built Environment.  The Institute will facilitate collaboration and information sharing between researchers and industry professionals, with the goal of researching, building, and promoting healthier built environments.  The Institute just hosted its #BuildHealth2018 Consortium meeting in Portland, OR, at which I presented some of the results from that large weatherization study regarding indoor plants.  The meeting was fantastic, and spurred in-depth discussion on problems facing industry professionals, innovative research goals, and a wealth of new possibilities.


In the past few months, I’ve spent a lot of my spare time helping to develop the Eugene Pod of 500 Women Scientists, an organization created to promote diversity, equity, and inclusion in science, and to promote education and interactive between scientists and the general public.  We have focused on hosting monthly Science Salon events, four to date, to do just that.  I presented at the first one, and have helped organize and MC the others.  The Eugene Pod’s activities were just featured on the central 500 WS page, as Pod of the Week, and you can also follow our updates and events on our Facebook page.

Running trivia on fire and fungi.


While it has been a struggle to maintain regular contributions, I still maintain Give Me the Short Version, along with a few intrepid contributors, which summarizes scientific articles for easier consumption.  This spring, I spent several days judging STEM and robotics competitions for several local Eugene middle and high schools, which has been a lot of fun.  The student projects are enthusiastic and creative, and I appreciate the chance to assist in these programs in some small way.


I have continued to mentor UO students.  The post-bac student from the BioBE lab that was learning bioinformatics with me, Mitch Rezzonico, was accepted to the University of Oregon’s Bioinformatics and Genomics Master’s Program!  Mitch wrapped up his work this spring to prepare for the intensive program, and with his interest in health research, BioBE hopes to work with him again in the future.  BioBE recently hired an undergraduate student for science communication, Mira Zimmerman.  Mira has been making some upgrades to the BioBE and ESBL websites which will continue to be rolled out over the next few months.  In addition, she will be helping me develop informative blog posts on the built environment, and helping to grow our information dissemination capabilities.  Hiring a student as a science communicator was something I had been hoping to test out, and so far it’s been a smashing success.


My course proposal for “Introduction to Mammalian Microbiomes” was accepted by the University of Oregon Clark Honor’s College for the fall term!

In April, I gave a guest lecture to Mark Fretz’s Design the Unseen course at the University of Oregon, on the Indoor Microbiome.  The class was populated by architecture students, who were learning about integrating health considerations into design strategies.  As a final project, students design a brief field experiment or intervention strategy for a design assistance project with Portland firms. I assisted one group in designing a small experiment on natural daylighting in an office and the effect on E. coli growth on culture plates – more on those results soon!


Later that same day, I have a lecture at the Oregon Museum of Science and Industry in Portland, as part of their OMSI After Dark series which opens the museum after-hours to adults for hands-on activities and lectures.  The lecture was on the gut microbiome, and I was able to present in the Planetarium!



I’ll be teaching “Introduction to Mammalian Microbiomes” this fall!

I’m very pleased to announce that I’ll be teaching a course this fall on “Introduction to Mammalian Microbiomes”, with the University of Oregon Clark Honors College.  I hope that this will be the first of many courses taught at UO, beginning with my background in “host-associated”, and expanding out into “house-associated”.

Course Description: Introduction to mammalian microbiomes.

The learning objectives of this course are to introduce students to basic concepts in host-associated microbiomes. Some background in microbial ecology, genetics, anatomy, bioinformatics, or immunology would be helpful, but is not required. While difficult concepts will be discussed, the course is intended to teach students about the basic principles: what is a microbiome? How does host anatomy drive microbial ecology? How does that community develop over time? How does it change? How does technology inform our understanding of these systems, and what limitations does that technology introduce? When we read about host-associated microbiomes in the news, especially regarding health, how can we assess if the study is rigorous and how should be interpret the scope of the findings? The skill-set objectives include learning to review complicated journal articles, distilling their findings while understanding their limitations, and developing science communication skills in a variety of formats.