Perspective on developing curricula

At the University of Maine, I am currently developing two new courses based on similar material I’ve taught previously at the University of Oregon and Montana State University. I’ve written about several of those classes, including a retrospective after teaching ‘Introduction to Mammalian Microbiomes’ to humanities students. Here, with the spring semester commencing this week, I thought I would share my approaches to developing coursework. While a class doesn’t stand on organizational physique alone, it can go a long way to facilitating your communication with your students, their understanding of course expectations, and their ability to assimilate the information you are disseminating.

Organization of materials

The nature of my teaching means means that I don’t assign readings from a textbook, I curate reading lists for my students from current scientific literature, which changes a little each year. Because of this, and the need for file management, I have a few tricks. First, I have a folder (on my computer and the online teaching tool) specific to readings for that class. I curate the file name with first author, year, and few words from the title so I can keep track of what it is (ex. Zhulin_2015_databases_review). I duplicate that file name in my syllabus, so I can copy and paste instead of writing it out again.

I format my syllabus as a table, and add each reading to the day on which it is assigned. If I move lectures around, I move the whole table row, so I can migrate assignments and readings along with lecture titles. Lastly, because the readings are specific to lecture and date assigned, I mimic that order in my file names by numbering them all instead of leaving them in alphabetic order (ex. 10_Zhulin_2015_databases_review), to facilitate knowing when and which is assigned.

And I don’t just number them by order, I number them by lecture so students or I can just match the lecture number across the lecture files, assigned readings, etc.

Written assignments (when logistically possible)

A stack of papers facedown on a table.

There’s no easy way to grade written assignments from students, but I prefer it to exam-style assessments. Particularly in teaching microbial ecology and sequencing data analysis, there’s not a lot of strict memorization like there is in anatomy. The material lends itself more to critical thinking and debating theory, to presenting a scientific argument, to problem solving, or to composing mock scientific manuscripts. In allowing students the word count to work through their thoughts, they are able to find the words to express their opinion on, say, the Hygiene Hypothesis when only weeks before they didn’t know that some microbes can turn the immune system on or off.

Written assignments allow me to give them feedback, including grammatical corrections, suggestion on sentence structure, pointing out leaps of logic where they left readers behind, and of course, on the strength of the scientific argument. This is particularly helpful when learning to write technical science.

Red pen.
Photo credit: Merriam-Webster

In giving students the agency to choose a topic to write about from the curricula tasting menu I’ve provided in my lectures, I receive back more information than just what I provided, which keeps things interesting for me. And, in giving them assignments which practice their writing voice, I witness their progression towards mature scientific writing.

Stacking assignments for improved retention

It takes time to become familiar with new information. That’s why school subjects are taught multiple times, or in specific orders, as you progress through education. I have 13 – 15 weeks in a semester (or 10 in a quarter!) to on-board students and teach them a skill. For most of the students I have taught, my class is their first introduction, or their first formal introduction, to the subject.

Especially for my host-associated microbial courses, there are hundreds of years-and-counting worth of history which led us to our current understanding of the microbes that inhabit us. Without that history, an explanation of the available technology, and a discussion of how that technology shaped the view we had, I can’t do justice to the majority of the coursework where I explain how we discovered the relationship between salivation and the microbial community geography in your mouth. The first section of my ‘host-associated’ course includes this background information, and a discussion of current technology, which is reiterated when later discussing literature and how technological shortcomings can hamper our understanding of a microbial community.

To give students more time to practice the material, I give related readings, have a guided discussion at the end of lectures, and stack assignments. Students start with a non-technical summary of a paper; 1-ish paragraph where they have to introduce the paper and why it was done, the methods used, and a major result or two. Trying to explain a complex experiment in simple terms is a great way for students to gain familiarity. When it comes time to write a two-page essay for a take-home exam, I allow the students to build off those summaries, if they choose.

An inclusive syllabus

A syllabus is a document which encompasses the important information for the class, including meeting times and rooms, grading policy, lecture and assignment schedule, required reading materials, and more. It can be used to recruit students to sign up for the class, and once in attendance, it’s the first impression students have. It’s where they refer for questions about the course, what’s expected of them, and where to find instructions on assignments. I write my syllabi in a way that makes sense to me, the instructor, and I welcome feedback from students when my instructions are confusing. But, I also welcome feedback from different student populations in order to make the language and presentation of the document more approachable. Sometimes you just need something to break the ice. Like a paper turkey hat.

Sue wearing a paper hat shaped like a turkey.
Wearing the turkey hat that my mentee and I made.

I haven’t actually worn a turkey hat to teach a class, that’s too informal. I dress up like an anatomically-annotated dissected cat, because I’m a professional. Or, I ran regular class discussions that occasionally got heated and were monopolized by a fraction of the class. The next year, I took a stronger moderator stance and would impose more restrictions (“Ok the next comment HAS to use the word “microbes”). I don’t like calling on students, so the next time I have discussions I think I’m going to give them all D20 dice and have them roll for initiative on the order of presenting comments. I also added this to my syllabi:

Class participation: Students are expected to participate in discussions in class.  I strive to create inclusive discussions, but if students still find it challenging to participate please notify me and I will alter the discussion format as needed.

AVS 590 Syllabus spring 2020

Most universities also require text or links to their campus policies, driven by federal, state, or university law. These include a statement about accommodations for disabilities, although many faculty are happy to make accommodations without the student receiving prior approval. I started allowing students to occasionally attend lectures by video conferencing, if they notified me ahead of time. It allowed students who were ill or traveling to keep pace with the material, and I have even remotely conference-videoed in to a student’s laptop to present when I was home sick but didn’t want to cancel class.

New this year, I’ve included text about students missing classes for parenting or caregiving responsibilities, something I don’t currently participate in, so it was not something I thought to include information on until someone else (Jenn Perry) gave me their perspective. Now I have this:

Pregnancy, lactation, and parenting: I am happy to make accommodations for students based on pregnancy, lactation, and parental needs, as well as work with the Office of Equal Opportunities. Maine state and UMaine policy allows students to breastfeed in any space, including in class. If a lactation space is required, please contact E.O. for arrangements.

AVS 590 Syllabus spring 2020

Similarly, a tweet by Dave Baltrus about including inclusive statements such as information for food insecure students led me to add this:

Food insecure? Need clothes? Check out the Black Bear Exchange’s Food Pantry: https://umaine.edu/volunteer/black-bear-exchange/ or Old Town Crossroads Ministry.

AVS 590 Syllabus spring 2020

And finally, I added text about mandatory reporting. As a public university employee, I am obligated to notify the University of Maine Title IX office about criminal actions towards or by anyone on campus. If a student reveals information to me, I have to pass it on to the Title IX office which will then discretely reach out to the student with resources. The office advocates for anyone on campus, but they are particular important in situations involving students who are low on the power scale and cannot advocate for themselves. While my door is always open to students looking for help, I felt it was important for them to know that I might not be able to keep the meeting confidential.

Inclusiveness in the classroom is important to me, because if students don’t feel welcome, comfortable, and free from hunger, they can’t learn. Despite what opponents think, this doesn’t involve “coddling” or “being too soft”. It means being realistic in my expectations about how people learn and what else they are dealing with that might be inhibiting that. It means that I learn to be more proficient at communication and personnel management, which are vital skills for academics. And it means that we all elevate our skills together.

Silhouettes of four people jumping in a dark cave.
Purple flower in front of a lake and mountains in the background.

Pod Coordinator for 500 Women Scientists, Orono!

I’m pleased to announce that I have been elected the Pod Coordinator for the Orono Pod of 500 Women Scientists! This spring, I hope to expand membership in and around Orono, connect with other inclusion and STEMM groups in Maine, and roll out some new initiatives and public engagement events.

500 Women Scientists is a non-profit, grassroots organization started by four women. Immediately following the November 2016 election, they published an open letter re-affirming their commitment to speak up for science and for all genders, minorities, immigrants, people with disabilities, and LGBTQIA. This commitment became a global movement, and that movement has blossomed into a formal organization dedicated to improving science communities. As of January 2018, 500 Women Scientists has over 20,000 members and supporters.

Building communities and fostering real change comes from small groups, not large crowds. Our local pods help create those deep roots through strong, personal relationships. Pods focus on issues that resonate in their communities, rooted in our mission and values. As women in science, technology, engineering and math, as role models to young girls and women, as leaders in our communities, we accept this challenge. Accept this challenge with us.

I was previously a Pod Coordinator in Eugene, where I coordinated group networking and public engagement events with a fabulous group. I’m looking forward to developing the same heartfelt connections here.

Featured Image Credit: 500 Women Scientists

Research article for young scientists published!

I tried something new last new, I helped rewrite an already published study into a version specifically for young scientists, aged 10-18. Ashkaan Fahimipour, the lead author on the original research article examining the effect of light on bacterial communities in household dust, brought up the idea while we were working together at BioBE.

The journal is called Frontier for Young Minds, and pairs a young scientist with an established scientist to review your articles, a ~1,500 word summary version. The journal provides cartoon illustrations that help bring your science to life.

Ours was written by an undergrad I was mentoring at UO, Sam Rosenberg, and architecture grad student Julia May helped us with our Figures. I wasn’t involved with the original article, but along with Ashkaan, I helped Sam draft the summary as non-technical summaries of highly-technical science can be a real challenge. Check it out!

Rosenberg, S., Ishaq, S., May, J., Fahimipour, A.K. 2020. How light exposure changes bacterial communities in household dust. Frontiers for Young Minds. Article.

UMaine Research Experience for Undergraduate (REU) summer 2020 program applications open til Jan 31, 2020.

The University of Maine Research Experience for Undergraduates (REU) program is accepting applications for their summer 2020 program. Apply by January 31, 2020!

Poster advertising the Research Experience for Undergraduates program at the University of Maine.

2019 Year In Review

Notwithstanding the different reasons, 2019 has left us reeling, myself included. Early in the year, I was left scrambling to keep my science career going in the face of unsteady funding resources. Through a combination of collaboration, long hours of writing, a strong support network, a lot of luck, and a pragmatic demeanor, I landed a tenure-track faculty position and pulled off one of the best years of my career, to date. I deeply appreciate all of the concern, assistance, coffee, revisions in a timely manner, coffee, and support provided by so many individuals in the last year.

View this post on Instagram

I got this official pin to wear to events!!

A post shared by Dr. Sue Ishaq (@dr.sueishaq) on

Research

My momentous research activity of 2019 was joining the faculty of the University of Maine, Orono, School of Food and Agriculture as an Assistant Professor of Animal and Veterinary Sciences, beginning in September. In August, my partner, our patient dog, and I drove from the west coast to Maine on a 9-day adventure that would begin a new (and more permanent) phase of our life. From our education in Vermont, to my post-docs in Oregon, to my research faculty position in Oregon, to Maine, we loved the opportunity to live in various states, but are looking forward to having an address for longer than 2 years and more stable income forecasting.

The first few months of my faculty position have been busy! Notably, it’s involved a LOT of training, paperwork, getting acquainted with campus resources, and making connections. Some of these have involved seeking approval to take on graduate students, not just from my department, but students from other departmental programs that want their research to center around my lab’s specialties. UMaine strives to provide interdisciplinary opportunities for students, and as such, encourage multiple cooperating positions. In addition to being able to bring on grad students through the School of Food and Agriculture, I have just been approved as faculty in the Graduate School for Biomedical Sciences and Engineering, and have another cooperating position pending.


My work now spans three major research priorities. My lab will focus on the gut microbiome of livestock, and how microbes can be used to promote animal health and production. This will take shape in a variety of ways, including through global collaborations (more on those as they develop, but many of my previous rumen collaborations that began at Montana State are included in that). I’ll be taking on several graduate and undergraduate students in 2020 for these projects.

Through ongoing collaboration on projects led by Drs. Fabian Menalled and Tim Seipel at Montana State University, I’ll be participating in research to understand climate change and farming practices on wheat production and soil microbes. I am a graduate committee member for Tindall Ouverson, who is completing her master’s at MSU.

I’ll also be collaborating with researchers on microbes in the human gut. Through ongoing collaborations with researchers at the Institute for Health in the Built Environment (primarily those at BioBE) at the University of Oregon, I’ll be looking at infectious disease transmission and building design. And I’m currently developing new collaborations with researchers at Husson University, University of Maine, University of Vermont, and other institutions, which will investigate the interaction between diet, gut microbes, and human health. I’ll be taking on several graduate and undergraduate students in 2020 for these projects.


I published a record 10 papers this year! I don’t expect to achieve this again anytime soon: over the spring and summer I was only working half-time, and with the rest of my time I was doggedly writing up previous project results, overseeing undergraduate authors, and emailing co-authors for revisions. Writing or managing the writing of a manuscript takes a significant amount of work. Even when experiments or field trials are completed within days, weeks, or months, it may takes years to process, analyze, and measure the samples you collect, as well as complete the statistical analysis. You might encounter technical problems, or need to validate a method for use with your research. After all, much of what researchers do is trying new things, as there isn’t always a well-validated protocol to follow and you need to come up with something new. Thus, at least half of the publications from 2019 were wrapping up experiments that had occurred as far back as 2014!

Because of the time span, it meant I published on a variety of topics, from the effect of diet on rumen bacteria in sheep, to the effect of farming practices on bacteria in soil, to the effect of chemicals from vinyl floors on bacteria in dust. It meant a LOT of reading for me, to appraise and condense the relevant literature for each project: my citations list might contain up to 100 other papers!

A stack of papers facedown on a table.

Teaching

Over the summer, I taught “Microbes and Social Equity” at The University of Oregon for the Clark Honors College. In just four weeks, the students, a few guest speakers, and I collectively wrote a paper to introduce the topic. We submitted it to the journal PloS Biology, and it was accepted for publication in their special call, Microbiomes Across Ecosystems. You can read it here. In the first month, it’s been viewed nearly 5,000 times!

I am developing new coursework for the University of Maine, including AVS 254 Introduction to Animal Microbiomes, which will be taught annually beginning in Fall 2020. This spring, I’ll be teaching a ‘special topics’ class, which will be the preliminary version of a class I am currently developing: DNA Sequence Data Analysis Lab, which will teach students the programming and analysis required to understand complex DNA sequence data, including amplicon, whole-genome, and metagenomics datasets. The special topics version is limited enrollment, and a way to beta-test the class before spending the significant amount of time required to develop a new course. I’ll be sharing more info about the classes as they develop.

Presentations and Travel

In May, I again presented my BioBE research to the Institute for Health in the Built Environment

Consortium meeting in Portland, OR. It was a quiet summer for me, but I did attend the Gordon Research Conference on Animal-Microbe Symbioses in Vermont, which showcased fascinating research on the ways that humans and animals interact with the microbes that inhabit our bodies. In October, I had a whirlwind week-long trip which involved giving a presentation in Monterrey, Mexico, then a different presentation in Reno, NV the following day, then heading to Bozeman, MT to catch up with collaborators and teach bioinformatics to Tindall. All of the meetings, seminars, and training was very valuable, but the best part, hands-down, was going to Matacanes canyon.

Sue rappelling down through a waterfall into a cave.
Rappelling down through a waterfall into a cave.

Outreach

Over 2019, I gave more than ten (not all have been published) interviews on my research! This included a live radio interview, and two podcasts: all new experiences for me.

  1. UMaine prof: Inequity is creating a gut microbe gap.” Mike Tipping and Ben Chin, Maine People’s Alliance. Dec 20, 2019.
  2. Women in Science – Implicit Bias“. Ida Hardin. Dec 13, 2019.
  3. Inequity takes a toll on your gut microbes, too.” Sue Ishaq,  The Conversation, Dec 4, 2019.
    1. Picked up by The Telegraph, Alton, Illinois, and other agencies
    2. Included on UMaine news
  4. All people have a right to healthy gut microbes.” Paige Jarreau and Signe Asberg, Lifeapps. Dec 3, 2019.  
  5. Rich People Have Access to Better Microbes Than Poor People, Researchers Say.” Becky Ferreira, Vice. Nov 26, 2019.
  6. Microbiome is a Human Right.” Heather Smith, Sierra. Nov 26, 2019.
  7. Life, liberty—and access to microbes?” Press release for Plos Biology. Nov 19, 2019.
  8. Study finds season an important factor in soil microbe sampling.” Erin Miller, University of Maine.  Nov 6, 2019.
  9. cUriOus: Buildings Have Microbiomes, Too!” The Jefferson Exchange with Geoffrey Riley. Mar 8, 2019.
  10. ” The Great Indoors: Interior Ecology Under the Looking Glass.” Alex Notman, University of Oregon College of Design. Jan 14, 2019.

Blog

I published 30 posts this year, including this one, although with ~11,000 words total, I had less to talk about. I anticipate that will change when my lab gets rolling. The most popular post this year continues to be Work-Life Balance: What Do Professors Do?, self explanatory, and the least popular this year is I Accepted a New Position in Soil Microbiology and Agroeconomy!, which makes sense as it was an announcement from 2016 about a post-doc position I’d accepted.

My site had its most popular year, with >4,000 visitors taking >6,000 views, represented by 109 countries. In total, my site has had > 10,000 visitors and >15,000 views since Jan 2016

Map of the globe with countries colored by number of visitors to this website.
Website visitors in 2019.

Life

If you’ve read this far, you can probably guess how hectic my life has been this year. At the same time, it’s been gorgeously complex. I finally made it down to see Crater Lake in Oregon, went powder skiing in the Rockies in Utah, drove through the dramatic beauty of the Rockies in Alberta, made my first visit to Mexico and was immersed in the isolated beauty of a mountain canyon in Matacanes.

Crater Lake, Oregon.
Crater Lake, Oregon.
Sue with her dog, Izzy.

I read the debut science-fiction novel of one very dear friend of mine and non-debut science non-fiction novel of another dear friend, and took an excessive amount of selfies with my dog.

Sue and Lee in front of a log cabin.

And… we bought our very first house!!

Looking Ahead

This Year in Review, I have the clearest idea of where my 2020 is heading. With a new lab and new classes, I’ll be happily well-occupied. I’ll be obtaining 3+ quotes to buy each piece of lab equipment (if it cost more that $6,000) and then waiting two months for it to arrive, troubleshooting R problems and revising scientific manuscripts written by first-time authors, I’ll be training my new brood of students in the lab, and I’ll be sharing my experiences here! Stay tuned!


Featured Image: Cookies from Mug Buddy Cookies

Joined the Faculty in the Graduate School of Biomedical Science and Engineering

Screenshot of  Dr. Ishaq's faculty profile page on the University of Maine Graduate School of Biomedical Science and Engineering website.

I have joined the graduate faculty in the Graduate School of Biomedical Science and Engineering (GSBSE) at the University of Maine. GSBSE is an interdisciplinary graduate program which spans not only multiple graduate programs at UM, but at four other institutions in the state. As faculty in the program, I can now accept graduate students whose research doesn’t fit under the umbrella of one specific field.

Podcast interview on the Maine Beacon

This week, I chatted with Mike Tipping, Communications Director of Maine People’s Alliance, and Ben Chin, Deputy Director of Maine People’s Alliance, on my recent publication on ‘microbes and social equity’ in PLoS Biology and the blog version found in the Conversation. We chat about social policies currently under discussion and how they can impact your microbes, why you should care about your neighbor’s microbes, and steps you can take to be a mire microbially-minded and socially-minded community member.

Check out the podcast here:

You can catch up on previous interviews at these fine outlets:

AVS 254: Introduction to Animal Microbiomes

My first official course at the University of Maine has been approved! Starting Fall 2020, I will teach AVS 254: Introduction to Animal Microbiomes!

This 3-credit course is geared towards undergraduates with a science background, with sophomore status or higher. Some familiarity with microbiology, genetics, mammalian anatomy, or microbial ecology would be helpful, but is not specifically required.

The working syllabus can be found here, with more information on lectures, assignments, workload, classroom policies, and more:

Description:  This course introduces students to host-associated microbiomes; the genomic collection of bacteria, archaea, fungi, protozoa, and viruses present in a host ecosystem. In each lecture, we will focus on an anatomical location, and discuss the host and environmental pressures which select for the resident microbial community.  The material is primarily in animals (mammals, birds, fish, amphibians) but includes some human-specific comparisons. This course will introduce ecological theories (e.g. environmental selection, neutral theory) in the context of microbial communities, the history of host-associated microbiology, and how technology has contributed to or limited our understanding of organisms and their critical role in our health and development. The skill-set objectives include group discussions, reading scientific literature, and scientific writing in a variety of styles and both technical and non-technical formats. 

DNA double helix with dollar signs as a nucleotide.

The cost of scientific publishing

I’ve published a lot this year. More than normal, since I had 5 months with extra time and the knowledge that I would not be able to devote time to old projects if I began a tenure-track position. It’s been wonderful to publish so many projects, especially ones that had been languishing. But publishing fees can be steep, and often the grant is spent out by the time you publish, leaving researchers struggling to pay to get their results out. The more prestigious the journal, typically; the higher the cost. This encourages many authors to turn to lower impact or less reputable journals, which in turn causes colleagues to be suspicious of the article and may hurt their ability to get more grant money or promotion. On top of the base article processing charge (APC), there may be additional fees to print color photos, supplemental information, or to make the article open-access (readable without a journal subscription).

I’ve published 10 articles in 2019, only a fraction of what I contributed to paying for (thank you, collaborators!!). All costs are presented as 2019 fees in USD. Some journals charge less if you are a member of their society, or have financial assistance, but I’ve included the prices we paid.


Animal: $2835 APC flat rate (includes open-access)

Basic and Applied Ecology: $2000 APC for non-members (includes open-access)

Buildings: $1006 APC (always open-access)

Geoderma: $3350 APC for open-access and $2052.30 for printing 6 figures in color.

Indoor Air: $4300 APC for open-access

Journal of Animal Science: $1300 APC ($100/page member price x 10 pages + $500 color figure charge)

Journal of Exposure Science and Environmental Epidemiology: $3760 APC (includes open-access)

PeerJ: $1095 APC (always open-access). PeerJ also gives discounts for acting as a reviewer, though not applied here.

PLoS Biology: $0 APC for essays because they are published in the magazine (always open access)

PLoS ONE: $1595 APC (always open-access)

Total cost: $21,241


Keep in mind, I’m an editor for two journals and a reviewer for over a dozen, none of which I get paid for. Initial reviews take 2-4 hours, and follow up reviews on revised manuscripts can take 1-2 hours per revision (usually no more than 2 rounds). Editorial takes 1-2 hours per manuscript total, depending on the ease of finding reviewers and the completeness of those reviews. I estimate I’ve provided $3,240 (net) in editorial and review services this year alone.

Microbes and Social Equity essay published!

I’m pleased to announced that the ‘microbes and social equity’ paper has been published as an essay in PLoS Biology, and will be included in their Microbiomes Across Biological Systems special issue.

In summer 2019, I developed and taught a course on ‘Microbes and Social Equity‘ to the Clark Honors College at the University of Oregon. The course assignments were literature review essays on various topics, which were compiled into a single manuscript as the group-based final project for the course. This large version is available as a preprint; however, the published version is more focused.


Framing the discussion of microorganisms as a facet of social equity in human health.

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

  1. Biology and the Built Environment Center,  University of Oregon
  2. Robert D. Clark Honors College, University of Oregon
  3. Department of Human Physiology, University of Oregon
  4. Charles H. Lundquist College of Business, University of Oregon
  5. School of Journalism and Communication, University of Oregon
  6. Department of Landscape Architecture, University of Oregon
  7. Counseling Psychology and Human Services, College of Education, University of Oregon
  8. Institute of Ecology and Evolution, University of Oregon

Abstract

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 focus on the argument that access to microorganisms as a facet of public health, and argue that health inequality may be compounded by inequitable microbial exposure.