Woman dressed in a costume of a dissected cat, to teach a class on Halloween.

Teaching students to give scientific presentations

This semester at UMaine, I’m teaching a section of AVS633/FSN671 Graduate Seminar, for students in the Animal and Veterinary Science and the Food Science and Nutrition grad programs. Naturally, I decided to spice up the course requirements.

In all the presentations I have given; during classes, teaching, as public lectures, guest seminars, and conference proceedings, I’ve faced a great deal of technical and audience-related challenges. There is a wealth of information on the formatting and content aspects of building a scientific presentation, but in my experience, that’s only half the battle. The other half is in being able to accurately and interestingly relay that information to your audience. Even in professional settings, I have faced disruptive technical failures that caused me to alter my talk or have to adjust my narrative, and I have fielded poorly-crafted or poorly-intended questions from my audience, all while trying to maintain my composure.

I felt that this was what the graduate students needed to learn, and in a safe space where it was OK to simply, well, give a bad presentation. To convey this, I put together an introduction to the class (below) and a series of assignments.

The Elevator Speech

Their very first assignment was to stand up, with notes but no slides, and give a 3 minute speech on a topic of their choice. It had to be non-technical, and designed to provide information in an approachable way such that the person stuck on the elevator with you would actually want to hear more. As academics, especially when you are a student, you often get caught up in repeating jargon or with having to explain yourself in highly detailed language to faculty who are training and testing you. You forget how to present your work to someone who has absolutely no background, and only a few minutes worth of attention span to devote to hearing about your very niche research question. To give an effective elevator speech, the students needed to distill only the critical information for someone to follow their line of thinking, and to not get bogged down by extraneous detail.

Peer Presentations and Awkward Audience Questions

For the second assignment of the course, each student was required to give a presentation on their research, their program of study, or a specific topic they were interested in and the relevant research. Due to the number of students and course time allotted, this presentation only needed to be 10 minutes long, but I’ve found it can be more difficult to present your material concisely. The students presented as if to a peer audience, so they could use a certain amount of jargon or introduce methods with minimal explanation. This style of presentation is common in graduate school, and as expected, the students all did incredibly well.

To add a challenge here, I instead focused on the audience (in this case, the rest of the class). The thing about being an audience member that most people never think about, is that you also need to conduct yourself with a certain level of professionalism. It might not be polite to shout a question or snarky response in the middle of a presentation, your comments might seem complementary but are in fact back-handed, or your question might simply be poorly crafted. I have been asked, or been witness to, a lot of poorly-worded audience questions and responses, and I’m not referring to general public audiences, I’m talking about academics who should know better.

To that end, for each student presentation, I gave an index card to another student in the audience to ask or perform during the talk. Participation was voluntary. Some of these are well-meant questions that are simply commonly asked. Others are silly, and some are rude. I didn’t include anything offensive or abusive, but those examples abound. The list is pretty funny, but please, NEVER DO THESE AS A REAL AUDIENCE MEMBER.

  • Ask the speaker if they will be a medical doctor (or veterinarian) after they finish this [research] degree.
  • State that you have a question. Then pose a statement/comment that is not a question.
  • Be on your phone (texting) or overtly not paying attention to the entire presentation.
  • Ask them to explain a simple concept that they covered in their presentation (but that you missed because you weren’t paying attention).
  • Cough or sneeze comically loud, or drop something during the presentation.
  • Ask the speaker how they chose this topic or how they got into this type of research/work. (This seems benign, but can take away from more specific questions during a peer presentation.)
  • Ask if the speaker is familiar with a field/event/discovery that is somewhat related to their presentation but not actually in their presentation.  Example, speaker presents about infectious disease in cattle and you ask them about “cow farts and global warming”.
  • Comment that the speaker looks really young for someone in their position.  Example: “Wow, I thought you were an undergrad! You look really young. I mean, that’s a compliment.”
  • Get up during the presentation and adjust the lights or shades in the room. You don’t have to make them better, just change them.
  • Ask the speaker a multiple part question. They can be simple questions, but ask them all in one, long, run-on sentence.
  • Begin your question with “As a parent,….” even if you are not a parent and the question has nothing to do with being a parent. 
  • Ask the presenter who analyzed their data for them (even if they have already said they analyzed it themselves).
  • Tell the speaker that their method is not valid (but don’t explain why).
  • Tell the speaker: “This was a pretty good presentation. When you have been in grad school a few more years I think you’ll be a really good speaker.”
  • Tell the speaker that this kind of work has been done before and ask what they have done that is unique.
  • Raise your hand to ask a question, but then sit back, squint your eyes, exhale loudly, pause for a moment, then say, “Never mind”.

The Technical Challenge

On multiple occasions, I have had to give a short (10 min) presentation by memory because the slideshow wouldn’t open or advance. I have had poor lighting, or poor color contrasting from the projector, which made it difficult to read my slides. I have had projection screens which were much smaller than I anticipated such that my text was too small to read on figures, and I’ve more or less given up the hope that I will routinely encounter “presenter mode” when using podiums or other people’s machines. I’ve had a projector that kept shorting out during the talk and creating blank screens for 10 seconds, something which you can hear me talk about in the lecture recording but not see on the recorded slides. I’ve had my available time cut in half, had to cut my presentation short because I included too much detail, realized I had poorly organized the presentation of material or forgotten to define a critical aspect, been unable to play videos or animations, had hand-held slide advancers with low batteries, had automatic slide advance turned on by mistake, and more.

When you face these surprises during a talk, you often don’t have the time, never mind the presence of mind, to resolve the problem. You simply have to make the best of it before your time runs out. It helps to know your material, but it also helps to be able to improvise, which is a skill best developed in practice. You might need to fill air time, or reconstruct your presentation on the fly, or make light of the situation to cut the tension in the room. To help my students prepare, I asked them to send me their peer presentation, as I wanted them to use a presentation they had just given and were familiar with. Then, I introduced mistakes into the presentation without disclosing what those might be, only that they would be there.

To think up enough technical problems I could use, I enlisted the help of scientists on twitter. Click on the Tweet below to find the thread and see the other contributions from @HannahMLachance, @canda007, @Wymelenberg, @vaughan_soil, @murphyc1928, @cskrzy, @maria_turfdr, @mcd_611.

I came up with this non-exhaustive list:

  • Replace a video with a still shot
  • Have 2 students make slides on the same topic, then have them present the other one’s slides (to simulate when a co-author gives you some slides on their contribution and you forget what they mean).
  • Reorder some of the slides
  • Remove a lot of the text on the slide
  • Resize images to be too small for audience to see resolution
  • Introduce blank slides to simulate projector connection issues (like screen flickering on/off occasionally)
  • Ppt won’t open at all or won’t advance beyond title slide
  • Change font on all text to tight cursive
  • No ‘presenter mode’ available
  • Resize slide dimensions and don’t adjust proportions to ensure fit
  • Turn laptop around so can’t see screen as if presenting at a podium
  • Add animations to everything
  • Add notification of email on timer (created a shape with animated pop in and out, as well as notification chime).
  • No photos
  • Slide advancer with poor quality batteries
  • Automatic slide advance

Public Presentations

Public presentations are an overlooked part of academia, but a crucial aspect. If you are at a public university, or you receive state or federal funding, your work is being supported by tax dollars. Many federal grants require an outreach or public education portion to your project, where you make the results available to interested parties (called stakeholders). Science communication is also extremely important in bridging the divide between scientific and public communities.

Public presentations need to present information approach-ably. I don’t mean they need to talk down to people, I mean they need to consider that the audience might not have a frame of reference for what you are talking about. I have a PhD, but it’s meaningless if I attend technical lectures on physics. For the third challenge in class, students can give their presentation again but with the knowledge that they can’t throw 20 slides worth of dense information at their audience, they can’t use technical language without defining it, and that sometimes the best way to explain complicated information is using pictures or analogies.

Update: In light of Corvid-19 concerns, campuses have been closing and switching over to remote instruction. This was rather challenging to do well with a presentations class, as giving a webinar isn’t the same as giving a public presentation. To be more creative, I am having students submit their public presentation slides online. I then assign them to another student, who has to annotate the ‘presenter notes’ with the speech of how they would present these slides. I then return the annotated version to the original presenter so they can see how well their slides spoke for themselves. In this “presentation telephone game”, I hope they will see how easy their slides were translatable to someone else, which is a common problem in slides put online without any notes or audio: so much gets lost when the presenter isn’t providing the information and filling in the additional information that is only briefly noted on the slides.

Learning (to Pretend) to Enjoy Giving Presentation

You can’t always control the technical aspects of your talk, or select your audience, or even be prepared for the weather that day. You won’t always be well-rested, or in good health, on the day of. Fun fact about stress, it can trigger spotting or early menstruation. There’s nothing quite as terrifying as being in the middle of your presentation when you are suddenly aware that you have a limited amount of time to get off stage and hope that there are feminine products available for free in the nearest restroom, because your women’s dress pants don’t have pockets for you to carry quarters for the dispensary machines.

You won’t always have time to prepare. Once, I had 5 minutes of notification that I would have to stand up in front of 50 – 75 other college students and Jane Goodall and present a recap on a service-learning course, at a time when I dreaded any and all public speaking. But you can’t really decline the offer to talk in front of Jane Goodall when she had taken the time and effort to be in the room to listen to you all. So you just have to stand up and start talking before you convince yourself you can’t do it.

You can have faith in yourself, know that you will try your best, and remind yourself that it will be good enough. I’ve been an audience member at perfect presentations, and I remember that it went really well and nothing at all about the content. The talks that I remember most are the ones where the speaker connected with me. They were funny, they were humanizing, and they took technical problems and awkward interactions in stride.

The best way to become a better speaker, I think, is to be open to the idea that you are going to mess up. A lot. But each time, you will learn from that experience, you will ask for feedback, and you get back out there. As academics, we have to present information on nearly a daily basis. It is, in fact, a significant part of the job. So instead of dreading it, we should at least pretend to enjoy it until, one day, we find that we do.

Image of plastic wrapped over soil to inhibit weed growth.

NE IPM funded collaborative proposal!

I’m pleased to announce that a small grant proposal I am part of was just funded by the Northeastern Integrated Pest Management (IPM) Center! The proposal, “A Working Group on Tarping and Soil Solarization”, brings together researchers and food production professionals from across New England to identify the current use of tarping and soil solarization to prevent weed growth without the use of chemcials, as well as identify barriers to adoption of this practice, and develop research proposals to fill any knowledge gaps related to the use of these methods and their effect on crop production, weed suppression, soil microbiota, and the local ecosystem.

Led by Dr. Sonja Birthisel (UM), the working group team is comprised of Dr. Alicyn Smart (UM), myself, Master Nathalie Lounsbury (UNH), and Eva Kinnebrew (UVM). We will be joined by over a dozen other researchers across New England who perform agricultural research, along with dozens of ‘stakeholders’: producers and other food production professionals who have an interest in the group findings and would make use of any knowledge we generate.

Featured Image Credit: Soil Solarization, Wikimedia

Blueberries on a bush

My first funded proposal at UMaine!

Now that I’m an assistant professor, a significant amount of my time is spent writing grant proposals to fund projects I’d like to do in the future.

Many large federal or foundational grants take up to a year from submission to funds distribution, and the success rate, especially for newly-established researches, can be quite low. It’s prudent to start writing well in advance of the due date, and to start small, with “pilot projects”.

To that end, I’m pleased to announce that Dr. Lily Calderwood and I just received word that the Wild Blueberry Commission of Maine is funding a pilot project of ours; “Exploration of Soil Microbiota in Wild Blueberry Soils“. We’ll be recruiting 1 – 2 UMaine students for summer/fall 2020 to participate in the research for their Capstone senior research projects.

Dr. Calderwood is an Extension Wild Blueberry Specialist, and Assistant Professor of Horticulture in the School of Food and Agriculture at UMaine. She and I developed this project when meeting for the first time, over coffee. We realized we’d both been at the University of Vermont doing our PhD’s concurrently, and in neighboring buildings! We got to chatting about my work in wheat soil microbial communities, and her work on blueberry production, and the untapped research potential between the two.

This pilot will generate some preliminary data to help us get a first look at the soil microbiota associated with blueberries, and in response to management practices and environmental conditions. From this seed funding, Lily and I hope to cultivate fruitful research projects for years to come!

Featured Image: Wild Maine Blueberries, Wikimedia

STEMMinists of Maine inaugural meeting announced!

One of the biggest challenges faced by STEMM (science, technology, engineering, math, medicine) advocacy groups is finding the time and resources to propose and execute initiatives, as well as find the time for social media engagement to grow the group. There are a number of groups already established in Maine which seek to promote STEMM advocacy/education, accessibility, diversity/equity/inclusion, campus community members, and the general public. 

STEMMinists of Maine is a newly-formed STEMM advocacy group, which seeks to bring together these various groups. Our goal is to act as an umbrella organization, to create a cohesive social media presence that makes it easier for people interested in STEMM advocacy and inclusion to find resources, coordinate events, and get the message out.  All participating groups will remain autonomous, but participation (which is free) will hopefully allow us all to reach a broader audience and have a greater impact in both campus and state-wide initiatives.

Our inaugural meeting will be held at the University of Maine campus, 57 Stodder Hall, to introduce STEMMinists and invite others to be part of our work to promote a better STEMM community. All are welcome!

Shortly after, our website and social media will be finalized and launched!

First official Ishaq lab meeting!

The Ishaq lab has been quietly growing, and we had our first official meeting today! I can’t wait to see what we accomplish together.

Screenshot of group meeting in a video conference call.
We are all such rock stars, we needed to meet virtually to keep up with our busy schedules!

Top left: Adwoa, a PhD student in Dr. Jen Perry’s lab, working on kombucha microbes. Top right: in the office with me, Alexandria, an MPS student working on research techniques for gut microbes. Bottom left: senior member Tindall, a MS student at Montana State University in the Menalled/Seipel lab working on soil microbes. Bottom left: Johanna, incoming MS student in nutrition who will be working on diet and gut microbes. Undergrad Emily couldn’t make it, and we have a few more pending members and affiliates joining us in 2020.

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