How does an academic department decide on their courses?

Now that I am an assistant professor, I perform scientific research, teach formal classes to undergraduate and graduate students, and I advise undergraduate students, as well as a smattering of other administrative or organizing-based activities. While I have performed nearly all of these in past job positions, the advising is a completely new aspect which has provided valuable insight into my other activities. The University of Maine serves a large number of undergraduate students, and many degree programs are specifically designed as preparation for specific career fields. Undergraduate students in my department now ask for my advice on which courses to take to best finish their degree, and this has led to some interesting discussions on why certain classes are required or not, and why certain classes are offered or not. I realized that the mechanics of course development are not well known to students, or even to academics who haven’t participated in it, and I thought I would share what I’ve learned.

Deciding on content

At the university level, courses are created and designed to offer a certain level of core material made up of basic concepts to introduce students to different fields of information; courses like introduction to biology, or general writing techniques. These may be referred to as ‘general education‘ courses and are designed for student audiences from many different programs at once. GenEd courses are taken in the first or second year of study in order to fill in any gaps from the very different high school educations students have, as well as teach the basics of information-finding and collaboration skills that they will need in other classes. GenEds are usually required before students take high-level courses in specific areas of study. Often, GenEds or introductory courses cater to hundreds of students per year, and there are several instructors to cover all the course sections, as well as teaching assistants, who provide instruction. There are additional core University requirements that each department can decide how to handle, such as the UMaine Capstone Experience requirement for students, which requires students to create a senior project related to their major. Within each academic department or unit (for example, Animal and Veterinary Sciences), there are core course requirements specific to that field of student that all students enrolled in that program need to take (for example, these requirements for Bachelor’s of Animal Science with a pre-veterinary concentration).

One factor in the decision about course content is simply which skills or knowledge students will need in order to enter the workforce related to their field of study. For example, undergraduate students who are intending to go on to a veterinary degree are often enrolled in pre-vet programs designed to prepare students for that further degree and to meet those application qualifications. As such, they will need to learn everything from anatomy to physics. Any content which is required to make the degree meaningful will also be required for students to pass in order to graduate, and means that it must be taught often enough that students have an opportunity to take it. Thus, core or required classes might be held at least annually, and sometimes multiple times a year. If the usual instructor is unable to teach it for a period of time, or there is turnover in the department, a temporary or adjunct instructor can be brought in on a short-term contract to ensure that course can be offered regularly.

Another factor is the area of expertise of the faculty instructors, who are research and/or teaching faculty with long-term contracts, such that those classes will be offered for at least as long as that person is employed. Because areas of expertise change over time, and because faculty come and go, this often drives the evolution of an academic department’s curriculum focus over decades. For example, I have a 50% research and 50% teaching appointment over a 9-month contract, which equates to 12 credits worth of teaching or formal mentoring in my department over the academic year. While I do teach some courses which were already set by the department, I had enough room in that 50% appointment to propose and teach two classes of my own design, one of which has now become a required course for animal science undergraduates specifically because my area of expertise has grown in importance and popularity in the past few decades. Departments will hire new faculty or instructors specifically because of their area of expertise and which direction they want the overall academic program to go in.

A more minor consideration on course content relates to university budget models, and whether academic departments get additional faculty or instructor salary for teaching students from outside their department – essentially a question of where tuition revenue is spent. Departmental course content is tailored to the intended student audience.  If a course is popular across the university but does not have applicability or appeal to the students within that faculty or instructor’s department, it can be difficult to justify spending time on it because most instructors or faculty are contracted to specific departments or academic unit budgets. However, a course with broad appeal could be taught outside of our contracted time, such as during winter or summer sessions, or potentially during the academic year as “overload teaching” which is above the number of credits outlined in our contact. This usually pays on top of the 9 or 12 month salaried contracts of instructors, but is restricted by the lack of free time that most faculty face.

Theory or approach to teaching

After settling on what should be taught, how, then, does a department decide how a class should be taught or constructed? How broad or specific should the information be, and how will the assignments or course requirements assess what students have learned? How will skills be taught? Broadly, this is called pedagogy: the method and practice of teaching, and is something which many faculty find themselves responsible for knowing even if we have not gotten an opportunity to develop our pedagogy in previous jobs. Prior to being an assistant professor at UMaine, I taught several different courses, including ones with pre-set materials that I re-hashed and presented in my own way, and ones with materials that I collected and decided entirely how to present (taught as electives). It wasn’t until that I was a long-term member of an academic department that I was able to participate in setting the direction of departmental courses, and to consider what we teach and how.  As part of my application to my current position, and my tenure packet (application to get a forever contract for my job), I am required to explain my teaching philosophy and how I put those ideas into practice in the classroom. I have previously shared some of those working documents.

As an example: it’s important to learn about how microbes affect animal health. Do I need to spend all my time lecturing to provide that info, or is there another format of information sharing I can use? I certainly need to lecture some, to introduce new topics or walk students through reading complicated graphs. But, it’s important that I also teach students how to find this information and assess it on their own, because they will be doing that for the rest of their life after they leave the classroom. Thus, I need to design my class materials and timeline to provide information and empower students to develop those same skills that I learned to get where I am: reading graphs, considering multiple and conflicting study results, forming questions and how to go about finding the answer. I might start a class with some lecture, followed by an assignment where students have to identity a question they have about microbiomes, then write down the expertise or people needed to find the answer from multiple perspectives, and finally outline what they thought that team could get done in one year.

Getting courses approved

There are many steps in the course approval process and, naturally, plenty of paperwork. In addition to a draft syllabus, a course proposal form is required which provides the logistical details (how many credits, lab or lecture, in person or online, and more), and describes the goals and scope of the content (introductory or experienced level), intended audience (students in which departments and which year of study), and how it will provide necessary skills or info to them. Importantly, the proposal form must describe how the new course will complement current courses that are offered at the University. Being able to show that there is a demand for this specific course, or that it is needed for professional development of the students, will support the course proposal during the approval process. This last part requires the person proposing the course to communicate with instructors of similar classes who might have students that will want to take this class. Are there aspects that you could include in your new course to make this more relevant to them, or to connect this new class to existing classes?

Once the proposal form is complete, it gets sent to the unit or departmental faculty committee for discussion, and may be returned for revisions. This committee might be made up of senior faculty in the department, or all the faculty if it is a small department. Not only can other faculty help improve the courses, but the time you spend teaching a course is time you can’t spend teaching other things that the department needs. So, your colleagues need assess whether this course is a good use of time and effort.

If the course is approved by the department, the proposal goes to the college curriculum committee which is made up of faculty from multiple different but related departments (for example, one from each department in the College of Natural Sciences, Forestry, and Agriculture). Often, faculty sitting on this committee are Undergraduate Coordinators in their own department, and have a lot of input into the scope of what undergraduates study.  After that committee, the proposal then goes on to the university curriculum committee to make sure it complies with university-wide standards and formatting. There are different forms and committees for undergraduate or graduate courses, and if you create a cross-listed course which can be taken by senior undergraduates and graduates, you’ll need to submit both forms and talk to both committee sets.

If a course is approved by the university, it will be assigned a number and will start appearing on the course catalogue. If the course is going to be required for students, though, it will usually be offered as an elective for the first year or even two before it is required for incoming students (current students can take it as an elective). Courses may also fulfil multiple requirements at once. For example, my AVS 254 Intro to Animal Microbiomes is required core subject material for AVS students, but also fills a university general education requirement to take a course that includes population and environment-scale information. In learning about the microbial communities, students also learn about microbial transmission between individuals, lifestyle choices and impact on host microbes, and interaction with the environment and affect on host microbes.

Matching faculty expectations to student experiences

An important consideration for course design is matching faculty expectations with student experiences. For example, the course materials which faculty see describe the course, but those faculty do not attend the course and experience how that information is shared. Thus, faculty may think that students are receiving information or skills, but the way that it is presented is not approachable or pertinent for students and they are unable to reuse what was presented in the course. Even faculty did audit a whole undergraduate course, we don’t have the same perspective that students do in that we might already be familiar with the material and we would not be able to identify where a lecture left out general information that would be critical for someone who is new to this. The student perspective is also driven by their need to do well in the course, not only by receiving a high grade but also by absorbing as much information which can help them in other classes or in their future career. Thus, aspects of the course which students think are interesting or important are not necessarily the same aspects that faculty identify as important.

Aligning the faculty and the student perspectives requires regular assessment of the course to make sure it is providing the necessary training and information to students. Often this assessment takes the form of faculty input and opinions, or changing needs of post-graduation industry career needs. It also relies on end of the semester evaluations of student performance (grades), and student feedback and evaluation of the courses. Student feedback can be unreliable when feedback on the course is preoccupied with comments which come from a place of personal bias or outright hostility. And, most course evaluations don’t provide enough granularity in the questions to thoroughly assess student perspectives on different aspects of the course, forcing students to give overall ratings. However, student feedback can be valuable when combined with other sources of information or asks more detailed questions.

To that end, Samantha Coombs, an AVS senior undergraduate researcher and I are designing surveys to gather student and faculty mentor perspectives for the UMaine AVS program Capstone Experiences courses, AVS 401 and 402. These courses are required for undergraduates to take to earn their bachelor’s degree, and require students to propose, conduct, and present results on research – often for the first time in their time at UMaine. If this wasn’t stressful enough, students typically work on projects which are part of faculty’s research portfolio,  and both students and faculty can be impacted by mismatches in expectations versus the reality of those collaborations. While we won’t be fully sharing the results of those surveys, we will be sharing summaries, and how the responses impacted future course materials in AVS 401 – the course in which students are first launched into research.

Improving the Curriculum for Future AVS 401 Undergraduates

Authors: Samantha Coombs and Dr. Sue Ishaq

Affiliations: School of Food and Agriculture at University of Maine, Orono

Keywords: Capstone, AVS 401, Undergraduates, Faculty, Stress, Mentor, Curriculum

Abstract

AVS undergraduates are not prepared to complete the requirements of AVS 401, before taking the course. In the AVS degree program, it is expected that undergraduates will gain knowledge, experience, and ideas to create a research project of their own. In many cases, AVS undergraduates are completing their capstones with never having performed a research project on their own. This is stress-inducing due to undergraduates having to learn both how to complete a research project, and how to write and complete a proposal. Undergraduates are given the choice to join a research project guided by a faculty mentor, but this leads to striving to meet expectations. Others struggle due to not knowing what project or path to go down. Each student needs a different situation that best fits their needs; this project will assist in trying to create a one-size-fits-all curriculum. The question I want to figure out is, can we adjust the curriculum in AVS 401 to meet the requirements of all AVS undergraduates for them to succeed in their capstone research? I hypothesize that we can create a curriculum that meets the requirements of undergraduates by surveying both faculty and undergraduates on their different expectations and experiences. Methods of research that will be conducted are, surveying AVS and other degree professors, surveying undergraduates who have taken AVS 401, reading syllabi, and reading scientific articles. The impact that this research will have is to create a class that is a one-size-fits-all for AVS 401 undergraduates. The curriculum will be adjusted due to the responses from both parties. The results will be a class that teaches undergraduates what they need to know to improve: the quality, efficiency, and reduce the stress of capstone projects.

UMaine REU ANEW program applications for undergraduates are open for summer 2022!

The University of Maine Research Experience for Undergraduates (REU) ANEW 2022 program is now open and accepting applications!  The REU program is intended to engage undergraduates in research, including those who have no or very little research experience.

Applications are currently being accepted for the REU ANEW summer 2022 program which is planned to be run in person from June 6 to August 12, 2022. Applications must be received by February 15, 2022 for full consideration. 

The website is updated with information for next year’s program and a new application form, or you can check out the attached poster:

The Microbes and Social Equity working group is turning 2!

It doesn’t seem that long ago that we were just an assorted group of interested researchers having a chat, but here we are two years later gaining international support and interest.  We greatly appreciate your interest in this group, and are pleased to share some of our recent updates.

We currently have 115 members of the Microbes and Social Equity working group, and another 33 people signed up just for the newsletter. In 2021, we ran a very successful speaker series, virtual symposium, and collectively had quite a few publications, presentations, and developments! We are excited to continue that momentum in 2022, and are planning another speaker series and virtual symposium, finalizing our journal special collection with mSystems, and furthering the collaborative projects we have begun. We will also be adding additional leadership roles for the group, to better accommodate our group and give more attention to our growing activities and initiatives.

Publications


mSystems Special Collections:

We are making great progress adding to our special collection with mSystem, with 3 papers published and several more currently in review! We will continue adding contributions through 2022. 

  1. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice | mSystems 
  2. Teaching with Microbes: Lessons from Fermentation during a Pandemic | mSystems
  3. Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome | mSystems  


Upcoming

  • Francisco Parada’s postdoc, Dr. Ismael Palacios-García finished collecting his probiotic/lifestyle randomized trial, collecting cognitive electrophysiology (EEG+EGG), microbial (DNA from fecal samples), and phenomenological data (questionnaires) over 4+ months. They hope they will be publishing some of these results soon!  
  • Jake Robinson is working on “Invisible Friends”, a popular science book anticipated for release in 2022. From Jake’s page: “Invisible Friends is about our extraordinary relationship with microbes, and how they shape our lives, our health, and the world around us. The book aims to challenge the prevailing negative perception of microorganisms, by highlighting the weird, wonderful, and indispensable roles they play in our health, behaviour, society, and ecosystems!”

Presentations

Upcoming: 

The Microbes and Social Equity speaker series 2022 is under development! We hope to invite speakers for a virtual series running January through April, Wednesdays from 12:00 – 13:00 EST. Registration is required but the series is free to attend.

inVIVO Planetary Health, virtual conference, Dec 1-7, 2021. Register here. Several MSE group members will be giving talks there, such as:

  • Sue Ishaq, “Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice”
  • Ari Kozik, “The human microbiome and health disparities: restoring dysbiosis as a matter of social justice”
  • Jake Robinson, “Microbiome-inspired green infrastructure (MIGI): a bioscience roadmap for urban ecosystem health”

2nd Rhode Island Microbiome Symposium, in person conference, University of Rhode Island Kingston, RI, January 14, 2022. Register here.

  • Sue Ishaq, ​”Microbes at the nexus of environmental, biological, and social research”

American Society for Microbiology (ASM) Microbe 2022, in person conference, Washington, DC (USA), June 9-13, 2022.

  • ‘Field Work & DEI Part 1: Fostering Equitable Partnerships with the Communities in Your Field Work Location’. The session’s date is June 11, 2022 (11:45AM – 12:30PM).
    • Ishaq,”Microbes and Social Equity: what is it and how do we do it?”
  • MSE special session, “Microbes and Social Equity: the Microbial Components of Social, Environmental, and Health Justice”. The session’s date is June 11, 2022 (1:45PM – 3:45PM), and the event is under development.
    • Featuring panelists Monica Trujillo, Ari Kozik, and Carla Bonilla

Past

Mike Friedman hosted a very successful MSE Special Session (together with the Microbial Ecology section) at this year’s virtual Ecological Society of America meeting. Naupaka Zimmerman, Justin Stewart, Monica Trujillo and Sue Ishaq gave short presentations on social justice and various aspects of environmental and human microbiota. But the bulk of the session was taken up by audience discussion of issues in environmental justice and microbes, practical and suggested policies and education.

Speaking in The Wildlife Society Nutritional Ecology seminar series!

I was invited to present a seminar in to the spring to The Wildlife Society Nutritional Ecology seminar series, and I’m honored to be part of an all-star line-up!! The talks being given from November through March, and you can find more info the TWS’ seminar announcement, which I have quoted below:

Please join The Wildlife Society’s Nutritional Ecology Working Group for our winter webinar series (https://wildlife.org/newg/webinar-series/). We will host virtual webinars at Noon (Mt Standard Time) on the second Wednesday of every month from 10 November 2021 – 9 March 2022. 

This year’s webinar theme is “The digestive biome and the influence of these organisms on nutrition and condition of wildlife.”  Our list of speakers this year are very diverse across many taxa!

Nutrition is vitally important for every life process of every living creature—from optimizing growth and reproduction to decreasing susceptibility to disease, predation, and death.  The science of nutritional ecology links food resources available to an animal with individual- and population-level performance, as well as to habitat- and landscape-level dynamics.  With data collected on nutritional requirements, food availability and quality, foraging and life history strategies under different environmental conditions, and body mass and condition, managers can predict how changes in one will impact the other. This provides a clear path for managing food resources in a way that optimizes population performance, or alternatively, for managing animal populations to optimize the health of ecosystems.  As global issues such as climate change, loss of habitat, and the spread of disease and parasites increasingly impact wildlife populations, the need for understanding the degree to which populations are limited by nutrition, and how we can best manage for nutrition, increases as well.

All webinars will be held at 12:00 pm Mountain Standard Time.  A flyer with zoom link will be sent out ahead of each webinar.

November 10th, 2021 – Jennifer Forbey – Boise State University. “Manipulating metabolites & microbes to manage wild herbivores”

 December 8th, 2021 – Kevin Kohl – University of Pittsburgh. “Who’s in charge here?: Microbial contributions to animal physiology, ecology, and evolution”

 January 12th, 2022 – Denise Dearing – University of Utah “Metabolic enabling and detoxification by gut microbes”

 February 9th, 2022 – Candace Williams – San Diego Zoo Wildlife Alliance. “Gut microbiota and their role in rhinoceros infertility”

 March 9th, 2022 – Sue Ishaq – University of Maine. “Moose rumen microbes and you”

For additional questions on the Nutritional Ecology Working Group, please visit our website (https://wildlife.org/newg/) or send us an email (tws.nutritional.ecology@gmail.com).  

The Wildlife Society

First first-authorship paper accepted for Olivia Choi from the Kamath Lab!

Olivia Choi, a doctoral candidate in the Kamath lab at the University of Maine, has had her first scientific paper accepted for which she is the first author – a position indicative of the amount of work and organization that she put into developing this work and wrangling the large research team involved. Olivia’s graduate work is winding down as she concentrates on writing up papers and her dissertation, and she is planning on defending her PhD and looking for a postdoc in 2022 in wild animal microbiomes and ecology.

Olivia brought this 16S rRNA dataset to use in my AVS590 data analysis class back in spring 2020, of bacterial communities in different locations on birds of different species, which had been sampled as part of her dissertation work on bird migration and range changes, microbial carriage, and risk of transmission of microbes to other animals. I mentored her through analysis and preliminary manuscript writing as part of that course. The research team generously invited me to join the author team, and I continued to provide mentorship as Olivia worked through the complex task of melding various types of microbiology data.


Choi, O., Corl, A., Lublin, A., Ishaq, S.L., Charter, M., Pekarsky, S., Thie, N., Tsalyuk, M., Turmejan, S., Wolfenden, A., Bowie, R.C.K., Nathan, R., Getz, W.M., Kamath, P.L. 2021. High-throughput sequencing for examining Salmonella prevalence and pathogen – microbiota relationships in barn swallows. Frontiers in Ecology and Evolution 9:681.

Abstract:

Studies in both humans and model organisms suggest that the microbiome may play a significant role in host health, including digestion and immune function. Microbiota can offer protection from exogenous pathogens through colonization resistance, but microbial dysbiosis in the gastrointestinal tract can decrease resistance and is associated with pathogenesis. Little is known about the effects of potential pathogens, such as Salmonella, on the microbiome in wildlife, which are known to play an important role in disease transmission. Recent studies have expanded the traditional use of 16S rRNA gene amplicon data from high-level characterization of host-associated microbial communities (i.e., the microbiome) to detection of specific bacteria. Few studies, however, have evaluated the ability of high-throughput 16S rRNA gene sequencing data to detect potential bacterial pathogens in comparison with laboratory culture-based methods. To address this knowledge gap, we evaluated the utility of 16S rRNA gene sequencing for potential pathogen detection and explored the relationship between potential pathogens and microbiota. First, we compared the detection of Salmonella spp. in barn swallows (Hirundo rustica) using 16S rRNA data with standard culture techniques. Second, we examined the prevalence of Salmonella using 16S rRNA data and examined the relationship between Salmonella presence or absence and individual host factors. Lastly, we evaluated host-associated bacterial diversity and community composition in Salmonella present versus absent birds. Out of 108 samples, we detected Salmonella in 6 (5.6%), 25 (23.1%), and 3 (2.8%) samples based on culture, unrarefied 16S rRNA gene sequencing data, and both techniques, respectively. In addition, we found that Salmonella presence and absence differed between birds based on migratory status and weight and that bacterial community composition and diversity differed between Salmonella present versus absent birds, with eleven bacterial taxa differentially abundant between the two groups. The results of this study highlight the value of high-throughput 16S rRNA gene sequencing data for bacterial pathogen detection and for examining relationships between potential pathogens and host-associated microbial communities. Further, this study emphasizes an approach using 16S rRNA gene sequencing data for simultaneously monitoring multiple pathogens in wild avian reservoirs, which is important for prediction and mitigation of disease spillover into livestock and humans. 

This work was presented at a recent scientific conference:

Choi*, O.N., Corl, A., Wolfenden, A., Lublin, A., Ishaq, S.L., Turjeman, S., Getz, W.M., Nathan, R., Bowie, R.C.K., Kamath, P.L. “High-throughput sequencing for examining Salmonella prevalence and pathogen -microbiota relationships in barn swallows.”  69th Annual – 14th Biennial Joint Conference of the Wildlife Disease Association & European Wildlife Disease Association. (virtual). Aug 31 – Sept 2, 2021.

Invited presentation about microbes and social equity this winter

Mark your calendars – I have been invited to give two presentations on microbes and social equity in general, and the MSE group in particular, this winter! Both events require prior registration.

You can also catch up with our recent publication as well as the other awesome work in the mSystems Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure.

 10th annual conference of inVIVO Planetary Health 

This year’s theme is Project Earthrise: From Healing to Flourishing for People, Places and Planet

1-7 December 2021. Virtual conference, with on-demand and live-stream content. Registration is required.

From the event site: “The meeting will bring together a tremendous network of like-minded people from diverse fields whose interests span from planetary/populationenvironmental health to microbial ecology/ systems biology and the deep biological mechanisms—all aiming to work in a more integrated systems framework as we seek to improve personal, environmental, economicand societal health alike. As always, our emphasis on meaningful collaborations and productive friendships as on the data and opportunities we generate.”

My talk title is pending.

2nd Rhode Island Microbiome Symposium at URI College of Pharmacy

14 January, 2022. In person. Registration is required.

From the event site: “The goal of this symposium is to promote microbiome and microbial research in Rhode Island and the Northeast by bringing together researchers from state universities and hospitals who currently work on microbiome research or who are interested in starting microbiome research.  We hope this symposium will stimulate networking and result in new collaborations, grant proposals and manuscripts.  While the scope is broad to encourage participation, the general focus will be on microbiome research relevant to the State of Rhode Island such as ocean health, aquaculture and precision medicine initiatives.”

Dr. Suzanne Ishaq
University of Maine
School of Food and Agriculture

Title: Microbes at the Nexus of Environmental, Biological, and Social Research

Invited Keynote Speaker

Dr. Ishaq received her doctorate in Animal, Nutrition and Food Science from the University of Vermont in 2015 where her graduate study focused on the rumen microbiology of the moose. She held post-doctoral positions at Montana State University, and a research faculty position at the University of Oregon. Since 2019, her lab in Maine focuses on host-associated microbial communities in animals and humans, and, how host and microbes interact in the gut.

In addition to her research on gut microbes, Dr. Ishaq is the founder of the Microbes and Social Equity working group. This group formed to examine, publicize, and promote a research program on the reciprocal impact of social inequality and microbiomes, both human and environmental. Membership is free and open to all.

Photo credit: Patrick Wine, University of Maine

Accepted into the first cohort of the UMaine EMPOWER Mentoring Program!

I’m pleased to announce that I was accepted into the first cohort of researchers for the new Enhanced Mentoring Program with Opportunities for Ways to Excel in Research (EMPOWER) at the University of Maine! We had our program launch yesterday, during which the 28 early-career researchers and their established-career mentors met to discuss the program goals, namely, to gain professional development in funding proposal writing and increase our success rate in an increasing-competitive research funding system.

Dr. Anne Lichtenwalner graciously accepted my request to act as my mentor for the program, which formalizes the mentorship and guidance she has voluntarily offered me without hesitation in my first two years at UMaine. Anne and I have also co-mentored four undergraduate students through their senior Capstone Experience research project in Animal and Veterinary Science. Over the next year, we will meet regularly to discuss and develop my research proposals related to animal health and microbiomes.

Welcome new Ishaq Lab members!

It’s a new school year, and that means new members have joined the Ishaq Lab team – primarily undergraduates in Animal and Veterinary Sciences who are participating in research in fulfillment of their Capstone Experience senior projects. Over the next few months, we’ll be sharing more details about our new team members and their projects.

While UMaine is back on campus, not all of our students are local, so we had a hybrid meeting of in-person and Zoom attendees. We have members at Husson University in Bangor, Maine; Tufts University in Medford, Massachusetts; and Stony Brook University in Stony Brook, New York!

We use collaborative file sharing such as Google Drive, virtual meeting spaces like Zoom, and messaging platforms such as Slack for a few projects to facilitate our research and keep track of information. To help us connect more easily, and especially to help get everyone in my office on screen together, we’ll be adding more virtual conferencing equipment, too.

Most of the Ishaq Lab Fall 2021 team were able to make it to a Welcome Meeting recently.

Listen to your microbes

Microbes are found everywhere, including on our skin or in our digestive tract, and the ones that hang out with us are called “host-associated”. Microbes interact with us in many different of ways, for better or for worse. To describe some common host-microbe interactions, the AVS254 Intro to Animal Microbiomes students collaborated on some playlists! Check them out on Spotify, and please note some songs are rated E for ‘explicit’ language. 

Pathobiont: Ever had a microbe that you thought loved you only to have it turn on you? This playlist takes you from besties to bacteriosis.

Symbiont: Sometimes you just can’t live without your microbes. Welcome to your happily ever after, even if it is a tiny one.

Exogenous: Sometimes hosts and microbes are like ships passing in the night. This playlist tells you about the microbe that got away.

Student point of view on researching microbes, flying squirrels, and mice around farms in Maine

Five women taking a photo together at a farm.  They are standing a few feet apart from each other, and standing in front of a cow feedlot with two cows eating.

This summer, a collaborative project was launched by the Ishaq Lab, Danielle Levesque, and Pauline Kamath at UMaine Orono and Jason Johnston at UMaine Presque Isle; “Climate Change Effects on Wild Mammal Ranges and Infectious Disease Exposure Risk at Maine Farms.”

Funded by the University of Maine Rural Health and Wellbeing Grand Challenge Grant Program, this project assesses pathogen carriage by mice and flying squirrels on or near farms in several locations in Maine. We live-capture mice and flying squirrels in traps, collect the poop they’ve left in the trap, and conduct a few other health screening tests in the field before releasing them. To maximize the information we collect while minimizing stress and interference to the animals, information is being collected for other projects in the Levesque Lab at the same time. We will be collecting samples for another few weeks, and then working on the samples we collected in the lab over the fall and winter.

One of the major goals of the funding program, and this project, is to engage students in research. After a few months on the project, some of our students describe their role and their experiences so far…


A close-up of a deer mouse sitting in a live capture trap in the forest.  In the background is one of the researchers kneeling on the ground.

Marissa Edwards

Undergraduate in Biology

Levesque Lab

Hi! My name is Marissa Edwards and I am an undergraduate research assistant with Danielle Levesque. This summer, my role has been to set traps, handle small mammals, and collect fecal and tissue samples from deer mice.

A pine marten sitting in a live capture trap in a forest.

One of the skills I’ve learned this summer is how to properly ear tag a mouse. To catch mice, we set traps across UMaine’s campus as well as other parts of Maine, including Moosehead Lake, Flagstaff Lake, and Presque Isle.

During our trip to Moosehead Lake, I saw a marten for the first time (it was in one of our traps). I did not know martens existed and initially thought it was a fisher cat. It was both a cool and terrifying experience!


Northern flying squirrel sitting on a net with a forest in the background.

Elise Gudde

Master’s Student of Ecology and Environmental Sciences

Levesque Lab

Hello, my name is Elise Gudde, and I am currently a master’s student at the University of Maine in the Ecology and Environmental Sciences program. I work in Dr. Danielle Levesque’s lab studying small mammal physiology in Maine.

Northern flying squirrel sitting on a net with a forest in the background.

This summer, as a part of the squirrel project, I work to trap small mammal species in Maine, such as white footed mice, deer mice, and flying squirrels in order to determine which species have shifted their range distributions as a result of climate change. Being a part of the research team, this summer has brought me all over Maine! I have been able to travel to Orono, Greenville, New Portland, and Aroostook County to study many interesting mammals. I even got to handle an Eastern chipmunk for the first time! As a member of the animal-handling side of the research team, I also collect fecal and tissue samples from the animals. These samples are then handed off for other members of the team to research in the lab!


Rebecca French wearing a white laboratory coat, a fabric face mask, and beige latex gloves while using a yellow plastic loop tool to spread bactrial cultures on fresh agar media plates to look for growth.  Rebecca is sitting at a biosafety cabinet with the glass window slide down between her and what she is working on.  Assorted scientific materials can be seen in the background.

Rebecca French

Undergraduate in Animal and Veterinary Sciences

Ishaq Lab

In the beginning of this project, I had no idea what I was getting myself into when I began researching flying squirrels and mice. I came into it with almost no in-person lab experience, so I had a lot to learn.

So far, I have been focusing on making media on petri dishes for culturing bacterial growth and after plating fecal bacteria on said plates; discerning what that growth can be identified as.

We are using media with specific nutrients, and colored dyes, and certain bacteria we are interested in will be able to survive or produce a color change. I have also been performing fecal flotations and viewing possible eggs and parasites under a microscope. What I’ve found most fun about this project is putting into practice what I have learned only in a classroom setting thus far. It is also very satisfying to be a part of every step of the project; from catching mice, to making media, to using that media to yield results and then to be able to have a large cache of information to turn it all into a full fledged project.


Joe Beale, posing for a photo in an open office space.

Joe Beale

Undergraduate in Animal and Veterinary Sciences

Kamath Lab

Hello! My name is Joseph Beale, and I am an undergraduate at the University of Maine working on the squirrel project as a part of my capstone requirement for graduation. My primary responsibility in this project is the molecular testing of samples obtained from the field. Primarily I will be working with ear punch samples taken from flying squirrels and field mice. DNA extracts from these field samples will be run via qPCR. The results of this qPCR will tell us if these squirrels are carrying any pathogens. 

The pathogens we will be testing for are those found in Ixodes ticks. The qPCR panel which we will be running the extracted DNA from the ear punches on tests for Borrelia burgdorferi, the causative agent of Lyme disease, Anaplasma phagocytophilum, the causative agent of anaplasmosis, and Babesia microti, the causative agent of Babesiosis. These pathogens and respective diseases discussed are all transmitted through Ixodes ticks. Deer ticks are the most common and famous of the Ixodes genus. The Ixodes genus encapsulates hard-bodied ticks. Along with deer ticks, Ixodes ticks found in Maine include: woodchuck ticks, squirrel ticks, mouse ticks, seabird ticks, and more. Mice and squirrel are ideal hosts for these Ixodes ticks, therefore becoming prime reservoirs for these diseases. In our research, we are interested in determining the prevalence of these diseases in squirrels and mice as these hosts can spread these diseases to humans and other animals in high tick areas. 

qPCR, quantitative polymerase chain reaction, allows for the quantification of amplified DNA in samples.  This will help tell us if these pathogens are present in samples and in what capacity. In qPCR provided DNA strands are added to the reaction. These strands match with the genome of the intended pathogens. If the pathogens are present in our samples, the provided DNA strands will bind to the present pathogen DNA. PCR will then work to manufacture billions of copies of this present pathogen DNA. 

When not working on this project, I also work in the University of Maine Cooperative Extension Diagnostic Research Laboratory as a part of the Tick Lab. In this position I have honed the molecular biology skills that I will in turn use for the squirrel project. 


Yvonne Booker

Undergraduate, Tuskeegee University

Levesque Lab

Microbes and the Mammalian Mystery“, reblogged from the University of Maine REU program.

Hello everyone! My name is Yvonne Booker and I am a rising senior, animal and poultry science major at Tuskegee University in Tuskegee, Alabama. I am interested in animal health research, with a particular focus in veterinary medicine. I’ve always wanted to be a veterinarian, but as I progressed throughout  college, I became interested in learning more about animal health and how I might help animals on a much larger and impactful scale–which led me to the REU ANEW program. Currently climate change is causing an increase in global temperatures, putting pressure on animals’ ability to interact and survive within their environment. Consequently, scientists are now attempting to understand not just how to prevent climate change, but how these creatures are adapting to this emerging challenge.

My research experience this summer is geared toward addressing this global issue. I am currently working in Dr. Danielle Levesque’s Lab, which aims to study the evolutionary and ecological physiology of mammals in relation to climate. My project involves conducting a literature review of the microbiome of mammals, to learn more about how their microbial community plays a role in how they adapt in a heat-stressed environment.

Our knowledge of vertebrate-microbe interactions derives partly from research on ectotherms. While this research paves the path for a better understanding of how organisms react to temperature changes, fewer studies have focused on how mammals deal with these extreme temperature shifts—specifically, the abrupt surge in climate change. The ability of endotherms to  thermoregulate alters our knowledge of (1) how mammals create heat tolerance against these environmental challenges and (2) how this internal process alters mammals’ adaptability and physiology over time. We suggest that the microbiome plays an essential part in understanding mammals’ heat tolerance and that this microbial community can help researchers further understand the various processes that allow mammals to survive extreme temperatures.

As a student of the REU ANEW program my goal was to go out of my comfort zone and study animals in an applied fashion that would impact animal health on an environmental and ecological scale; and this program was just that! My mentor, Dr. Levesque was wonderful in guiding me through conducting this research, while giving me the independence to create my own voice. The program directors, Dr. Anne Lichtenwalner and Dr. Kristina Cammen, have also  been extremely supportive throughout this entire program equipping students with the tools they need to succeed as researchers. Although research was my primary focus this summer, some of my favorite memories involved building community with the students and the staff. From weekly check-ins on zoom to virtual game nights of complete smiles and laughter, this program has been one for the books! The One Health and the Environment approach to this Research Experience for Undergraduate students has encouraged me to build on my curiosity within the field of science, and I’m looking forward to applying what I’ve learned to my career in the future.