A few weeks ago, I sat down with Sheba A-J, one of the producers of the WeTalkScience podcast, to talk about one of my recent publications in the research journal iScience, at which Sheba is also an editor. Listen to find out how lobsters are like humans, how I got involved on a project working with ants and nematodes, and how you can help make science a more welcoming place.
The full publication is:
Ishaq, S.L., A. Hotopp, S. Silverbrand, J.E. Dumont, A. Michaud, J. MacRae, S. P. Stock, E. Groden. 2021. Bacterial transfer from Pristionchus entomophagus nematodes to the invasive ant Myrmica rubra and the potential for colony mortality in coastal Maine. iScience 24(6):102663. Article.
A collaborative pilot project was funded by the Maine Food and Agriculture Center (MFAC) to investigate Vibrio bacteria in scallop hatcheries in Maine! This will support some ongoing work by a collaborative research team at UMaine and the Downeast Institute, as we develop a long-term, larger-scale project investigating scallop health and survival in hatcheries, something which will be critical to supporting sustainable and economically viable aquaculture productions.
“Investigating microbial biofilms in Maine hatchery production of sea scallop, Placopecten magellanicus.”
Principal Investigator: Sue Ishaq
Dr. Tim Bowden, Associate Professor of Aquaculture, University of Maine
Dr. Brian Beal, Professor of Marine Ecology, University of Maine at Machias; and Research Director/Professor, Downeast Institute
Dr. Erin Grey, Assistant Professor of Aquatic Genetics, University of Maine
Project Summary: Atlantic deep-sea scallops, Placopecten magellanicus, are an economically important species, generating up to $9 million in Maine alone. Despite their potential to the aquaculture industry, hatchery-based sea scallop production cannot rely on the generation of larvae to produce animals for harvest. In hatcheries, the last two weeks of the larval maturation phase is plagued by massive animal death, going from 60 million scallop larvae down to a handful of individuals in a span of 48 hours. This forces farmed scallop productions to rely on collection of wild scallop spat (juveniles), but wild population crashes, habitat quality, harvesting intensity, and warmer water temperatures threaten the sustainability and economic viability of this industry. The reasons for sea scallop larvae death remain unknown, but other cultured scallop species are known to suffer animal loss from bacterial infections, including from several bacterial species of Vibrio and Aeromonas. At the Downeast Institute in Beals, Maine, biofilms appear on tank surfaces within 24 hours. Routine screening for the presence of Vibrio sp. in tanks at DEI reveals no obvious signs of colonies in scallop tanks. Preliminary culturing and genetic identification from these biofilms suggests a species of Pseudoalteromonas, known biofilm formers which outcompete or inhibit other microorganisms. Our goal is to investigate the dynamics of tank surface biofilms in bivalve aquaculture facilities. Our long-term goals are to understandmicrobial community assembly and animal health during scallop hatchery production, and to standardize management practices to enhance the success of cultured scallop production.
“The Cornell Institute of Host-Microbe Interactions and Disease (CIHMID) is accepting applications for the NSF-funded Microbial Friends & Foes Research Experience for Undergraduates (REU) Summer Program (bit.ly/REU-CIHMID). Applications are due February 1, 2020.
The Microbial Friends & Foes Program will take place from June 8 to August 14, 2020. The program will provide training in the concepts and experimental approaches central to understanding microbial interactions with eukaryotic hosts. Students will learn about broad diversity of microbe-eukaryote interactions through conducting independent research projects, participation in weekly research group meetings, seminars presented by CIHMID faculty, Microbial Friends & Foes Synthesis Panels, CIHMID Summer Symposium, and Microbial Friends & Foes Poster Session. Emphasis will be placed on appreciation of the scientific method and developing effective strategies for conducting research as well as on the synthesis of concepts important to interspecific interactions across diverse systems. In addition, workshops in electronic database literacy, science citation software, research ethics, science communication, and planning for graduate study will be offered to the Microbial Friends & Foes program participants. Students will receive a stipend of $6000, travel subsidy, meal allowance and on-campus housing. Applicants will be asked to identify 3 laboratories of interest, and will be selected in a two-step review process by the program organizers and potential mentors. A flyer describing the program is attached and more information can be found at bit.ly/REU-CIHMID.
WHO SHOULD APPLY
*All undergraduate students interested in understanding microbial interactions with eukaryotic hosts.
*Members of minorities underrepresented in science, undergraduates from small colleges, and first-generation college students.
*Applicants must be United Stated citizens or permanent residents and at least 18 years old.”
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!
Last night, I gave my first “science stand-up” as part of the Oregon Museum of Science and Industry (OMSI) Science Pub series at Whirled Pies in Eugene, OR. I really enjoy giving public presentations of my work, and while I’ve been on stage with a microphone before, it was the first time I got a stool to put my drink on.
I gave a talk which encompassed much of my previous work on host-associated microbiomes in moose and other ruminants, as well as more current research from others on the human gut. It’s difficult enough to fit the field of host-associated microbiomes into a semester-long class, nevermind an hour (I digress), so I kept it to the highlights: “A crash course on the microbiome of the digestive tract“. You can find the slides here: Ishaq OMSI SciPub 20180208, although there is no video presentation at this time. I was honored to have such a well-attended lecture (about 120 people!) with an engaged audience, who had some really on-track questions about the intersection of microbial diversity and health.
As I’ve discussed here before, academic outreach is a sometimes overlooked, yet nevertheless extremely important, aspect of science. The members of the general public are a large portion of our stakeholder audience, and outreach helps disseminate that research knowledge, facilitate transparency of the research process, and engage people who might benefit from or be interested in our work. As I told the audience last night, scientists do like when people ask us about our work, but “we’re more scared of you than you are of us”. I encourage everyone to add science to their life by getting informed, getting involved, and getting out to vote.
Thanks again to OMSI for inviting me to participate, and to Whirled Pies for hosting!
As a thank you, I received this awesome pint glass!