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.

A close-up picture of petri dishes containing a light yellow film of microbes.

Rebecca received an undergraduate research award!

Rebecca French, an undergraduate researcher in Animal and Veterinary Science, is beginning her time in the Ishaq Lab with an auspicious start: she has been awarded a 2021 research award from the J. Franklin Witter Undergraduate Research Endowment Fund! The fund supports AVS undergraduate student involvement in faculty supervised research which involves the J. Franklin Witter Teaching & Research Center.

Rebecca’s project will involve zoonotic disease tracking in rodent populations that live near farms/human development versus those which live in more natural areas, and will take place at the Witter farm and a paired natural ecosystem. Her project is part of a larger collaboration between myself and a team of researchers, which was recently funded by the University of Maine, but which has not yet been announced (details soon).

Rebecca formally joined my research lab in February of this year, but I have had the pleasure of teaching her in my data analysis class since January, which will be a handy skillset later in the project. She also learn and perform microbial culturing, qPCR, Sanger sequencing, and even some animal trapping, handling, and identification; mammal physiology data collection and analysis.

Rebecca French

Undergraduate Researcher, Animal and Veterinary Sciences

Rebecca is an animal and veterinary science student with a concentration in pre-veterinary medicine. She joined the Ishaq lab team in 2021 as a part of her capstone project, which is focused on flying squirrels and mice that are carrying zoonotic pathogens into Maine.

A clock with wings flying in the air, with another one in the background out of focus. The background is a blurry tan.

Reflecting on “suggested deadlines” for assignments

Over the Fall 2020 semester, I changed my assignment deadline policy, creating “suggested deadlines” instead of enforced ones. I altered the language to “suggested deadline” in my syllabus semester timeline (in which I provide due dates for all assignments), I left submission portals open in the online teaching software, and I did not manually penalize grades for lateness. I made the change out of practicality for the fall semester, and I was personally pleased by the results; however, I wanted to hear from students. After being able to formally obtain student feedback during course evaluations, I wanted to reflect on that change and how I will implement it in future courses.

Previously, when grading policies were up to me, I accepted late assignments with a possible -10% grade penalty reduction per day, although I would waive it for a variety of circumstances. It was easy to enforce using online teaching software which timestamped submissions. This policy seemed to motivate some students, but in retrospect, it made students feel like they had to share their reasons for lateness and justify why they needed an extension. Not only did this late assignment policy increase the number of emails I received and time spent replying that yes, I would still accept it, but it also meant that students were sharing more personal information with me. I suspect that students who did not ask for deadline extensions probably had a reason but didn’t want to share than information in asking for an extension, and really, it is none of my business what else is going on in their life.

However, I made the decision to allow any assignments to be turned in after the due date without a penalty, in part because the pandemic shifted the amount and type of work most students were doing. Many of them reported an increased workload, having to attend remote classes in their car, trouble with internet access with so many other users on their network, and of course, power and internet outages are common in Maine when trees topple utility lines. If I had enforced assignment deadlines, then a third to a half of my students were in danger of failing the course because of lack of work, but not because of poor quality of work. This was unreasonable to me, especially in my undergraduate research course where I would be effectively be penalizing students for delays caused by their research mentors or haled research on campus.

So, I made the decision to trust my students to manage their own motivations and time management. After all, they are legal adults, they are not first years, and they have chosen to continue their education despite the financial burden and other constraints. More than that, almost all of my graded assignments with significant weight in the class are essay based, which means I can get a feel for the students’ writing voice and it is really easy to identify plagiarism by the change in tone or maturity of the writing. If being able to turn in an assignment late meant students’ could copy each other’s assignments, I should be able to catch it even without the online plagiarism checking software.

I was concerned that I would receive all the assignments on the very last day, and was dreading the avalanche of grading that would unleash on me. Instead, assignments trickled in on a regular basis, several hours to several months late depending on the students’ circumstances, some of which were later disclosed to me. Instead of getting sloppy, thrown-together assignments, I think the quality of writing and the depth of student critical thinking were improved. Students later reported being able to spend more time on the assignment when they had control over when that time could be spent. And, despite having the most students in the most difficult semester to get through, I discovered no instances of plagiarism.

I think I will make the move to suggested deadlines semi-permanent (some deadlines will be enforced based on if it is time-sensitive). The online teaching software I use can be set to assign a 0 to missing assignments, to email me when submissions are received, and to add conditions to submission portals, such as having first submitted another assignment or having received feedback on a previous assignment (like a previous draft of a paper). I can schedule automatic email reminders about assignments, email only students who are missing assignments, and students can check their grades and assignment lists online at any time. Not only does this dramatically reduce the time I spend chasing after assignments, but it gives students more agency in being able to participate in the class on their own time.

Certainly not every class can be structured this way or allow for flexible deadlines. But, I think a lot of them could be, and I think in most cases it would improve student engagement and learning outcomes. Below, you can find the comments on my two fall course evaluations, and you can check out my previous posts on curricula development or my teaching statements.


For much of the fall semester, assignment deadlines were open ended. Do you think keeping open ended deadlines (as in, you turn in things when they are ready but [not] on a specific date) next year would make this class better? Do you think you would be able to keep up with assignments without deadlines? Or do you think the deadlines help keep you on track?

My question from the course evaluations for this fall

Comments

  • I think the soft deadlines kept me in check, however it’s nice to know that if things unexpectedly get crazy for me that I won’t be penalized for taking extra time to make sure that I submit quality work.
  • I very much appreciated the flexibility in deadlines for this class as many other classes ramp up at the end of the semester. I felt as though I could control my workload with the assignments set up like this, and would recommend keeping the deadlines as suggestions to where you should be up to date in the course, but the actual submission deadline remains later in the semester.
  • You could do once a month check ins or something to verify nobody is completely slacking off. Maybe have three major deadlines to force people to keep up – one at the end of October, end of November and then the final submission?
  • The deadlines really helped keep me on track. Dr. Sue Ishaq was more than lenient with due dates and the work load, so I do not think anyone would have an excuse to not do well in this course (although this was really helpful with the troubling times humanity is facing). I think being more strict would be more fair to her as a professor and would help students not take advantage of being able to put things off and not learn the material.
  • I think the open ended deadlines was really helpful. It allowed me to put the time in when I could rather than rushing to get it done and turned in for the due date.
  • I appreciated having the due dates so I could try to get stuff in at a reasonable time but also that the deadlines were flexible so if something came up I wouldn’t turn in something I wasn’t happy with. I had a different class with no deadlines and it was horrible, I need the structure to be there but to also have the leniency for when things aren’t going well.
  • In this new quarantined world, the open deadlines were essential to academic success. While I didn’t struggle in this class necessarily, I did struggle in chemistry, pre calculus and lab with out the aid of study groups, math labs, and lab partners. Having open dead lines in this course not only affected my academic success in this course, but it also snow balled in a positive way and helped my GPA overall.
  • I think open ended deadlines with a suggested deadline would be the most helpful, because it will reduce the stress of deadlines, and allow for leeway in the case of multiple courses having work do on the same day, but it also gives a time frame around when the work should be done
  • The lack of deadlines required self–discipline but also removed the daunting aspect of the due date, which I often find myself deterred by and ultimately more likely to put off the work. I felt that the assignments were more inviting this way.
  • I think that this semester it was very beneficial to have the open ended deadlines. For me personally, I prefer to have deadlines to keep me on track, but I appreciate the flexibility of the open–ended deadlines.
  • I think having the open ended, suggestive deadlines made for a much easier semester. It took off a lot of stress to know that I could have an extra day if needed. Sometimes we get peaks in the semester where we’re slammed with work and knowing that if I needed an extra day or two to complete an assignment was really reassuring.
  • Thank you for being understanding on deadlines as this semester has been crazy, although the soft deadlines kept me on track without penalizing me for taking extra time if needed.
  • I think ended open deadlines do help due to things become crazier as the whole covid thing continues
  • I feel that open ended deadlines next year would make this class better because due to recent events in the world it is sometimes difficult communicating with project mentors. By having open ended deadlines, I know when it is supposed to be due, but if I am missing some information from someone on the project I do not worry as much about getting in trouble for handing it in late.
  • yes this is hard to juggle long term projects with weekly class deadlines. So open ended is the best for this class.
  • I believe the structure of fall semester deadlines was great.
  • I feel like open ended deadlines are very helpful because you would be able create better quality work with your research. I feel like I would be about to keep up with work without deadlines or just create the deadline for the end of the semester and put reminders.
  • I think a more strict set of deadlines could’ve been helpful as far as tracking progress. Exceptions could still be made for those struggling on a topic, or who are unable to start for some reason out of their control.
  • This semester, while everyone has been adjusting to the new way of pandemic life, the open ended deadlines were extremely helpful and stress relieving.
  • yes I think there should be soft deadlines, there is a date that it should be done but we didn’t have to have it done by then
  • Having a general guideline about when things should be turned in has been helpful, but keeping the deadlines open ended has relieved a lot of stress and has enabled me to produce better work because I was not rushed.
  • The deadlines kept me on track and having no deadlines would have me just turn everything in at the end which is bad.
  • I liked the deadlines. I would have kept all the work till the last minute if we didn’t. However, the open ended deadlines meant that even if you were behind, you wouldn’t be penalized which really helped.
  • I think open ended deadlines are a great idea because it allowed me to not feel pressured to submit something that I did not feel was ready. Without that stress, I was able to submit all of my assignments on time with the open ended deadline and not during the later one, which was helpful!

Featured Image Credit

“Now what? Science journeys into host associated microbiomes”

With the closing of the fall semester, I said goodbye to the students in my AVS 254: Introduction to Animal Microbiomes class. Despite the challenges and turmoil of fall 2020, these students have been engaged, enthusiastic, and creative. After presenting lectures on the microbial communities in and on animal hosts and how they can impact health and fitness, for the final class of the semester, I wanted to close with perspectives from the broader world of science.

To that end, I compiled several videos of “science journeys”, as told by active researchers in host microbiology, with an introduction to the class/video and my own science journey. I hope to compile a new volume each year I teach the class, to gather diverse paths.

I am extremely grateful for the time, effort, and thoughtfulness of the researchers who were able to contribute during a hectic semester to volume one:

  • Edna Chiang, University of Wisconsin Madison, @EdnaChiang  
  • Dr. Kaitlin Flynn, Benaroya Research Institute in Seattle, @microkaitlin  
  • Kiran Gurung, University of Groningen, @kirangurung29  
  • Jocelyn R. Holt, Texas A&M University, @JocelynRHolt  
  • Chissa Rivaldi, University of Notre Dame, @Powerofcheez  
  • Dr. Laura Tipton, Chaminade University of Honolulu, @lauraomics  
  • Dr. Benjamin Wenner, The Ohio State University, @Bynjammin

Reblog: “Animal and veterinary sciences seniors: Capstone stories”

Starting this fall, I have been teaching the UMaine Capstone Experience courses for Animal and Veterinary Sciences students (AVS 401 and 402). To complete the University of Maine requirements for graduation, students must participate in a Capstone Experience to knit together the work of their undergraduate degree into a cohesive project. AVS students are required to part pate in research under researcher mentorship. Some of those students felt comfortable sharing short descriptions of their project. The slightly edited summaries and my intro were posted to the University of Maine news page for teaching experience updates.

All 3 UMaine undergrads in the Ishaq Lab made Dean’s List Spring 2020 !

Congratulations to all three University of Maine undergrads in the Ishaq Lab for making the Dean’s List in Spring 2020: Jade Chin (AVS), Nicholas Hershbine (EES), and Emily Pierce (AVS)!!

Note, the Bowdoin Dean’s List is announced annually in the fall.

New course approved: AVS 454-554 DNA Sequencing Analysis Lab

A second course that I developed was accepted at the University of Maine! AVS 454-554 DNA Sequencing Data Analysis will be offered to undergraduate and graduate students starting Spring 2021.

AVS 454-554 teaches bioinformatics using DNA data. Starting with raw DNA sequencing data, students go through the process of quality assurance, statistical analysis, graphics design, as well as drafting a scientific manuscript. The course integrates research into teaching by using unpublished data, ideally data the students bring from their own research projects. Not only do students learn highly sought-after analytical and scientific writing skills, but it makes them active participants in research and their own learning. Most of the course time and skillset are focused on amplicon sequencing data, but we’ll also dabble with whole-genome, metagenomics, and metatranscriptomics.

Along with my Introduction to Animal Microbiomes course, I hope to get students interested in microbial ecology earlier in their studies, such that they have time to get involved with microbial ecology research in Maine in time for them to develop a Capstone research experience around it in their senior year. And what a coincidence, I’ll be teaching the Capstone courses for AVS (401 and 402) starting in fall 2020, as well.

This course is based on the precursor version, AVS 590, which I taught as a small, special topics version in the 2020 spring semester. And, even that is conceptually based on a lab section I taught at Montana State University in 2015 and 2016. DNA data analysis and I go way back.

Photo credit: Tom Rayner, Tenure Chasers

It can take several months to get course proposals approved, especially if you are proposing they meet general education requirements, are listed as required for a major degree, or have other levels to them. I started Sept 1, and the AVS faculty curriculum committee, the first step in the approval process, was meeting in early October. I didn’t have time to develop two course proposals in time, so I first proposed my data analysis course as a “special topics” version. These versions are offered selectively and are not counted the same way as an approved course. But, it gave me time to shore up my teaching materials, and teach several students who were graduating and couldn’t wait another year to learn these skills.

DNA sequencing data analysis is challenging to teach as well as to learn, but once over the learning curve, it can be extremely fun and rewarding. I’ve previously taught bioinformatics to undergraduates, and have or continue to publish with a number of them. In AVS 590 in the 2020 semester, there were 4 datasets being analyzed, and 3 of those led to manuscripts which are anticipated to be submitted to for review in scientific journals sometime this year!

R coding group at the University of Oregon, 2018

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. 

Application open for the Microbial Friends & Foes Research Experience for Undergraduates (REU) Summer Program at Cornell.

Poster describing The Cornell Institute of Host-Microbe Interactions and Disease (CIHMID) program for Microbial Friends and Foes Summer Program.

“The Cornell Institute of Host-Microbe Interactions and Disease (CIHMID) is accepting applications for the NSF-funded Microbial Friends & Foes Research Experience for Undergraduates (REU) Summer Program (bit.ly/REU-CIHMID).  Applications are due February 1, 2020.

The Microbial Friends & Foes Program will take place from June 8 to August 14, 2020.  The program will provide training in the concepts and experimental approaches central to understanding microbial interactions with eukaryotic hosts.  Students will learn about broad diversity of microbe-eukaryote interactions through conducting independent research projects, participation in weekly research group meetings, seminars presented by CIHMID faculty, Microbial Friends & Foes Synthesis Panels, CIHMID Summer Symposium, and Microbial Friends & Foes Poster Session. Emphasis will be placed on appreciation of the scientific method and developing effective strategies for conducting research as well as on the synthesis of concepts important to interspecific interactions across diverse systems.  In addition, workshops in electronic database literacy, science citation software, research ethics, science communication, and planning for graduate study will be offered to the Microbial Friends & Foes program participants. Students will receive a stipend of $6000, travel subsidy, meal allowance and on-campus housing.  Applicants will be asked to identify 3 laboratories of interest, and will be selected in a two-step review process by the program organizers and potential mentors. A flyer describing the program is attached and more information can be found at bit.ly/REU-CIHMID.

WHO SHOULD APPLY

*All undergraduate students interested in understanding microbial interactions with eukaryotic hosts.

*Members of minorities underrepresented in science, undergraduates from small colleges, and first-generation college students.

*Applicants must be United Stated citizens or permanent residents and at least 18 years old.”