I am pleased to announce that several PLoS journals are teaming up for a special issue, titled “Microbiome Across Biological Systems”, and the call for submissions is open!
PLoS (Public Library of Science) is a non-profit publisher that fosters open-access and accessibility in science, with a variety of subject-specific journals, as well as the interdisciplinary journal, PLoS ONE. I spend a lot of my time with interdisciplinary science which doesn’t quite fit with any one field, and I appreciate journals which are interested in that intersectionality. In fact, that’s what this call is about: looking at whole microbial communities at the intersection of ecosystems, at multiple trophic levels, and where the science is interdisciplinary.
The picture is just one instant in an event involving hundreds or thousands of organisms that were all doing a lot of different things, sometimes for just a few seconds. How would you describe it?
Maybe using the number of members present in this community? Or a list of names of attendees? The 16S rRNA gene for prokaryotes, or the 18S rRNA or ITS genes for eukaryotes, for examples, would tell us that. Those genes are found in all types of those organisms, and is a pretty effective means of basic identification. But, it’s only as good as how often that gene is found in the organisms you are looking for. There is no one gene that’s found exactly the same in all organisms, so you might need to target multiple different identification genes to look at all the different types of microorganisms, such as bacteria, fungi, protozoa, or archaea. Viruses don’t share a common gene across types, to look at viruses you’d need something else.
From our identification genes we could identify all the organisms wearing yellow; ex. phylogenetic Family = Ducks. That wouldn’t tell us if they were always found in this ecosystem (native Eugene population) or just passing through (transient population), but we could figure that out if we looked at every home game of the season and found certain community members there time and again.
But knowing they are Ducks doesn’t tell us anything else about that community member. What will they do if it starts raining? Are they able to go mountain biking? Perhaps we could identify their potential for activity by looking at the objects they are carrying? That would be akin to metagenomics, identifying all the DNA present from all the organisms, which tells us what genes are present, but not if they are currently or ever used. It can be challenging to interpret: think of sequencing data from one organism’s genome as one 1,000,000-piece puzzle and all the genomes in a community as 1,000 1,000,000-piece puzzles all dumped in a pile. In the crowd, metagenomics would tell us who had a credit card that was specifically used to buy umbrellas, but not whether they’d actually use the umbrella if it rains (ex. Eugeneans would not).
We could describe what everyone is doing at this moment. That would be transcriptomics, identifying all the RNA to determine which genes were actively being transcribed into proteins for use in some cellular function. If we see someone in the crowd using that credit card for an umbrella (DNA), the receipt would be the RNA. RNA is a working copy you make of the DNA to take to another part of the cell and use as a blueprint to make a protein. You don’t want your entire genome moving around, or need it to make one protein, so you make a small piece of RNA that will only hang around for a short period before degrading (i.e. you crumpling that RNA receipt and throwing it away because who keeps receipts anymore).
Using transcriptomics, we’d see you were activating your money to get that umbrella, but we wouldn’t see the umbrella itself. For that, we’d need metabolomics, which uses chemistry and physics instead of genomics, in order to identify chemicals (most often proteins). Think of metabolomics as describing this crowd by all the trash and crumbs and miscellaneous items they left behind. It’s one way to know what biological processes occurred (popcorn consumption and digestion).
From a technical standpoint, researching a microbiome might mean looking at all the DNA from all the organisms present to know who they are and of what they are capable. It might also mean looking at all the RNA present, which would tell you what genes were being used by “everyone” for whatever they were doing at a particular moment. Or you might also add metabolomics to identify all the chemical metabolites, which would be all the end products of what those cells were doing, and which are more stable than RNA so they could give you data about a longer frame of time. Collectively, -omics are technology that looks at all of a certain biological substance to help you understand a dynamic community. However, it’s important to remember that each technology gives a particular view of the community and comes with its own limitations.
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
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.
Over the fall 2018 term, BioBE and ESBL undergrads made a project video explaining a recent publication on the effect of different daylight treatments on bacteria in dust. The post and video can be found here!
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!
No one is sorry to say goodbye to 2018, yet it still seems like the 2018 Year in Review has arrived too soon. As usual, I’ve been keeping busy; you can find my reviews for 2017 and 2016 in the archives. For the first year in the three years since I started this blog, I’m not starting a new job! I’ve been at BioBE for a year and a half, and it’s a relief to be in an academic position long enough to finish the projects you started (I’m only just starting to submit some manuscripts for work I did back in Montana).
Two papers of mine were published this year, including one on the bacteria along the GI tract of calves, one on the effect of dietary zinc on bacteria in sheep. A comprehensive culturing initiative of rumen microorganisms, called the Hungate 1000 Project, an international initiative to which I contributed data, was also published. That puts me up to 17 scientific articles, of which 9 are first-authored, as well as 5 scientific reviews. I have three manuscripts in review right now, and another five being prepared – 2019 will be a busy year.
I joined two journal editorial boards this year, PloS One and Applied and Environmental Microbiology. Both positions are as an Academic (or handling) Editor; I will oversee manuscript review by soliciting reviewers, assessing their recommendations, and interfacing with authors. In recent years, the gender discrepancy in science has received more attention, and some journals are making efforts towards increasing the number of female editors, reviewers, and contributors to reduce implicit bias in science publishing. I am pleased to be in a position where I can help change that!
I’ve been spending a lot of time writing grants and developing potential projects on microbiology and health in the built environment, many of which should be moving forward in 2019. I’ve also been spending time training the 9 undergraduate students I hired over the summer and fall to work at BioBE. In addition to microbiology and molecular biology laboratory skills, I have been training them on DNA sequence analysis and coding, scientific literature review, and science writing and communications.
This fall term, I taught Introduction to Mammalian Microbiomes for the University of Oregon Clark Honor’s College. I proposed this new course last year, and developed the curricula largely from scratch. I’d previously taught some of the subject material at Montana State University in Carl Yeoman and Seth Walk’s Host-Associated Microbiomes course; however in IMM I was teaching to non-science majors. The course went well, and I’ll be diving into it in detail with a full blog post in a few weeks. I proposed the course again for next year, as well as another new course; Microbiology of the Built Environment.
Presentations and travel
Early in the year, I gave two public talks on the gut microbiome for Oregon Museum of Science and Industry; one in Eugene and one in Portland. Both were a lot of fun, and I really enjoyed getting to share my work with the public.
At the end of the spring term, I also presented at the University of Oregon IDEAL Framework Showcase. Over the 2017/2018 academic year I served on the Implicit Bias working group, tasked with assessing the need for campus-wide training and making recommendations to the college.
In June, I attended the HOMEChem Open House at the UT Austin Test House, University of Texas at Austin’s J.J. Pickle Research Campus. I got to tour the amazing indoor chemistry labs there, and met with BioBE collaborators to discuss pilot projects exploring the link between indoor chemistry and indoor microbiology.
MoBE 2018 was an intensive meeting that brought together the top names and the rising stars of MoBE research. Gordon conferences are closed-session to encourage the presentation of unpublished data and ideas, and to facilitate discussion and theoretical contemplation. While in Biddeford, I had the opportunity to eat seafood, visit friends, and check out Mug Buddy Cookies!!
Immediately after MoBE, I flew to Philadelphia for the Indoor Air 2018 conference. I again presented some of the work I’ve been part of, exploring the effect of weatherization and lifestyle on bacteria indoors. I also found some incredible shoes.
I spent a great deal of 2018 participating in activities for 500 Women Scientists. I am a Pod Coordinator for the Eugene Pod, and as such I meet regularly with other Coordinators to plan events. The majority of our 2018 events were Science Salons: science talks by local female researchers around a particular theme, with a hands-on activity to match, and a Q&A session about life as a (female) scientist. We heard about some awesome research, raised $1300 for local science non-profits, and learned how to be better community members by sharing personal stories about the triumphs and troughs of being a woman in science.
We also hosted a film screening of My Love Affair with the Brain, generously lent to 500WS by Luna Productions, followed by a panel discussion of women neuroscientists here in Eugene.
Along with two other Eugene Pod Coordinators, I wrote a small proposal which was funded, to coordinate workshops at UO: “Amplifying diverse voices: training and support for managing identity-based harassment in science communication”. Those workshops will take place in 2019.
I again participated in citizen science through Adventure Scientists, as part of their wood crews for the Timber Tracking 2018 campaign. Lee and I drove around a 20,000 sq mi section of southwestern Oregon to collect samples from big leaf maple trees at 10 locations which adhered to certain sampling parameters. Despite the large number of big leafs in Oregon, the sampling criteria made it difficult to find the perfect tree in an entire forest, and we logged a lot of mileage. Lee and I also volunteered for their Gallatin County Microplastics Initiative while we lived in Bozeman, MT.
As of today, my site received 4,447 view from 97 countries and 3,101 visitors in 2018. So far, I’ve published 109 posts, and received 6,147 visitors who viewed the site 9,481 times.
It’s easy to forget how many life events go by in a year, unless your social media is making you a video about them. But they were all important parts of my life and had some impact, however negligible, on my work. The one I’m most proud of was officiating the wedding of two dear friends, in Vermont.
I tried to spend more time on creative projects, including getting back into art after more-or-less tabling it for several years.
As usual, 2019 promises an abundance of opportunities. Already, I am planning out my conference schedule, seeking speakers for upcoming 500WS Science Salons, and writing, writing, writing. But through all of it, I will be trying to cultivate a more open, inclusive, and supportive work environment. In 2018, after more than a decade of trying to convince doctors that I should have agency over my own organs, I was finally approved for the hysterectomy that I’d wanted for so long, and the medical diagnostics to show that I’d actually needed it for probably just as long.
The surgery has dramatically improved my quality of life, and the scars are a constant reminder that you never know who is dealing with something in their life that isn’t visible to you, who is trying to pretend they aren’t in pain because they can’t afford to take time off to resolve their situation. At first, I kept the details to myself and I kept it off my professional social media. I did share, in exquisite detail, on my personal social media, and was flooded with similar stories from other women. It encouraged me to share a little more, after all, if I’d had surgery on a knee or a kidney I would talk about it openly, why not a uterus?
In a typical semester, one to two-thirds of the students that I teach or mentor will disclose that they experienced a serious life event, most often while at school. They may casually joke about how they couldn’t get time off or almost failed out that semester, or recall how receiving help saved them. I take my role as an educator, mentor, or supervisor seriously – the competition in academia forces students to work long or odd hours, to prioritize other things over study, to accept positions of low or no pay “for the experience”, or to accept professional relationships where they are not respected or may be taken advantage of. I have always tried to be a supportive mentor to students, but the higher up the ladder I climb the more important it is for me to set a good example for these students who will one day mentor people of their own.
In addition to listening to them, and having frank conversations, my response this year has been to get rid of student employee deadlines whenever possible. We are asked to do so much with our time in school, or in academia, but there are so many hours in the day. Sure, I routinely wish things were accomplished more promptly, but I have never once regretted not causing someone to have a breakdown. And constantly telling my students to take care of themselves first and work second reminds me to do the same, it benefits my work , and it’s made a certain furball very happy. Happy New Year!
Last year, one of my former research groups at Montana State University was awarded a USDA NIFA Foundational program grant, and I am a sub-award PI on that grant. We’ll be working together to investigate the effect of diversified farming systems – such as those that use cover crops, rotations, or integrate livestock grazing into field management – on crop production and soil bacterial communities: “Diversifying cropping systems through cover crops and targeted grazing: impacts on plant-microbe-insect interactions, yield and economic returns.”
The first soil samples were collected in Montana this summer, and I have been processing them for the past few weeks. I am using the opportunity to train a master’s student on microbiology and molecular genetics lab work.
Tindall Ouverson started this fall as a master’s student at MSU, working with Fabian Menalled and Tim Seipel in Bozeman, MT. She’s an environmental and soil scientist, and this is her first time working with microbes. She was here in Eugene for just a few days to learn everything needed for sequencing: DNA extraction, polymerase chain reaction, gel electrophoresis and visualization, DNA cleanup using magnetic beads, quantification, and pooling. Despite not having experience in microbiology or molecular biology, Tindall showed a real aptitude and picked up the techniques faster than I expected!
Once the sequences are generated, I’ll be (remotely) training Tindall on DNA sequence analysis. I’ll also be serving as one of her thesis committee members! Tindall will be the first of (hopefully) many cross-trained graduate students between myself and collaborators at MSU.