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

2020 Year In Review

As has become a New Year’s Eve tradition, here is the Ishaq Lab’s Year in Review for 2020! In previous years, I remarked on difficult and delightful times alike, but 2020 has been a year full of intense loss for so many, and some have unfairly borne more of that heavy weight. In reflecting on whether to go ahead with the post for this year, I chose to do so and to include a tone of optimism and hope because, for the first time in the Ishaq Lab, I am not writing the story of me, I am writing the story of we. Even though we couldn’t all be together this year, the Ishaq Lab has tried to do our best to stay connected, and I have had the pleasure of watching my new lab team work together and grow as scientists. I am proud of how they have handled this year, and I wanted to share their triumphs.

Research

2020 was the year for launching the first official projects of the Ishaq Lab, including a field project, a mouse project, and a handful of data analysis or microbial community projects.

A screenshot from a virtual lab meeting, featuring 5 women.

Early in the year, students began joining the lab, and we had our very first lab meeting, featuring Adwoa Dankwa (UM Perry lab), Alex Fahey (in the office with me), Tindall Ouverson (MSU, Menalled/Seipel lab), and Johanna Holman. Ironically, we had our first lab meeting over Zoom to facilitate students in multiple geographic areas, not suspecting we would only have virtual lab meetings this year.

The first field project was a literal one – a soil project! Because of the pandemic response in the spring and early summer, laboratory work was reduced until we could do so safely in enclosed spaces. But, we were able to launch a field project because the samples could be collected and processed by one person alone over the summer. Undergrad Nick Hershbine, who is majoring in Ecology and Environmental Sciences, has been investigating the microbial community in blueberry soil from farms around Maine. This is part of a larger project led by Dr. Lily Calderwood, and is supported by the  Wild Blueberry Commission of Maine (“Exploration of Soil Microbiota in Wild Blueberry Soils“). Nick is in the process of data analysis and interpretation, and we hope to write up the preliminary results over the winter.


The Ishaq Lab also launched its first mouse project! This is my first time managing mice, and luckily I have expert collaborators at Husson University and a stellar grad student taking the lead on those portions. I’ll be overseeing the microbial ecology aspects, done by master’s student Johanna Holman for her graduate work. Joe Balkan, a Biology undergrad at Tufts University, has been reviewing previous literature for culturing protocols, and will be joining us for two weeks over break to help with some bacterial work. Undergrad Evan Warburton, who started in the fall semester, will pick up that microbiology work from Joe at the beginning of the spring semester.

The Ishaq Lab also had its first student presentation this year, by master’s student Sarah Hosler giving a graduate seminar on her proposed research for her degree, which involves host-microbial interactions in ruminants. The first portion of laboratory work for her project will take place starting in winter break. We’re not ready to share any details, but first we will be trying out some new methodology, as well as recreating some older methodology which has fallen out of fashion.

As part of that first step, Sarah will be assisting with the Capstone project of undergrad Emily Pierce, who was awarded a UMaine CUGR undergrad fellowship to fund her work this spring. Emily will be investigating host-microbe interactions during Cryptosporidium parvum infections, something which routinely devastates newborn livestock. We had anticipated running this experiment last summer, but postponed it for safety. Emily and master’s of professional studies Alex Fahey have made good use of that delay, however, and have been spending the time reading scientific manuscripts, assembling experimental protocols, and designing their project. Alex does not need to complete a thesis for her degree, it’s more about assembling a variety of skills, so she has participated in a number of supportive activities this year.

Undergrad Jade Chin has been working on her Honor’s Thesis project, the scope of which has had to nimbly pivot over the past year as we weren’t sure what we would be able to accomplish during the pandemic. For example, we spent two months waiting for DNA extraction kits to arrive due to supply shortages and the federal disruption of the postal service. Those kits are critical to the very first step of the experimental procedures and one we could not skip. Jade will defend her Honors thesis in spring 2021, including a written thesis, an oral presentation, and even a short interview with her thesis committee, although it will be less formal and less strenuous than a graduate-level defense.

Grace Lee, an undergrad at Bowdoin College, has been working on data analysis of microbial communities associated with lobster in aquaculture, which is part of a larger project by Drs. Debbie Bouchard, Jean MacRae, and Heather Hamlin. The dataset is a large and complicated one, though with an elegant experimental design. We anticipate writing up the results beginning this winter and continuing through the spring. Grace will be joined by an undergrad who I have been mentoring in my AVS 401 Capstone class, who will be contributing a literature review for the manuscript.


Three papers were published this year, which were all part of previous projects at former positions. This included the culmination of my post-doc work in the Menalled Lab from back in 2016, and one of the small projects I participated in while at BioBE from 2017 to mid 2019.

  1. Horve, P.F., Dietz, L., Ishaq, S.L., Kline, J., Fretz, M., Van Den Wymelenberg, K. 2020. Viable bacterial communities on hospital window components in patient rooms. PeerJ 8: e9580. Article.
  2. Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Dryland cropping systems, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities. mSphere 5:e00340-20. Article.
  3. Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Soil bacterial communities of wheat vary across the growing season and among dryland farming systems. Geoderma 358(15):113989. Article. This was accepted in 2019 but not officially published till 2020.

It’s very common to have a slump in publications when starting a new position, and particularly when that involves moving to a new institution and establishing a new lab group. Research can take awhile to gain momentum, especially when you need to recruit and train new lab members. Or, when those lab members have to pause their lab work for global public health reasons. The Ishaq lab isn’t worried, we’ll make up for it in 2021. With all the ongoing projects, we anticipate a handful of other papers being developed next year. I’ve also got four manuscripts that have been in review for months, a process which has also been (understandably) delayed because of the pandemic.

Five stickers advertising the Ishaq Lab, with different photos of lab equipment, bacterial culture plates, and sheep.
We tried out some designs for Ishaq Lab stickers!

Teaching

I taught three new classes this year; one that was new to me and two that I developed myself. In spring 2020, I taught a special topics version of my DNA sequencing data analysis class, which means that I got provisional approval to teach it as a one-off while I completed the full course approval. Because the data analysis class is cross-listed for undergraduate seniors and for graduate students, it needed to go through two different curricula approval processes, and curricula must be approved a certain amount of time before the first instance of the class. That class has now been formally approved as AVS 454/554. From the spring version, two scientific manuscripts are in review, and a third is in preparation while more data are added. We managed to achieve a lot in the spring class, considering halfway through the semester we switched to remote instruction only as the early throes of the pandemic descended.

The other two new classes I taught this fall, including the first part of the Animal and Veterinary Sciences Capstone Experience, AVS 401, which instructs students on writing and presenting research proposals and matches students with a research mentor to try and complete the project. It was particularly challenging to do that this fall, when many researchers still had their work on pause because of the pandemic. I’ll be continuing this class in the spring as AVS 402, in which students present what they’ve done. While only a few AVS students will pursue research as a career, they will all need to implement the scientific method and the ethos of research into their lives no matter where they end up. Being able to find, assess, and critique information are all critical skills which this Capstone Experience helps them to develop.

I taught AVS 254, Introduction to Animal Microbiomes. I’ve previously taught some of this material, but to very different student audiences, which required a lot of course development on the fly over the semester. Even with the previous material, I still needed to revise all my previous lectures to adapt to a new lecture length, add new ones to make up about half the semester, and, as our understanding of host-associated microbiomes evolves over time, the course materials needed to be updated (annually) to present up-to-date knowledge. The last lecture of the semester was a compiled video of ‘science journeys‘, featuring researchers in host-associated microbiology sharing what they work on and how they got here. You can watch the video, too!

I also spent a lot of time this fall curating the Teaching Statement portion of my tenure packet, some of which I shared as a series of posts this fall. Next spring I will have my third-year review, which will be the first official hurdle and where I get more substantive feedback from my peer committee about the trajectory of my teaching, research, and outreach as I develop my packet to apply for tenure in ~ year 5. In 2021, I have a planned blog post describing the history and process of tenure, and I will likely share other portions of my tenure packet, such as my research statement.

Presentations from my couch

As I recently posted, 2020 has been The Year of The Virtual Conference. Many conference in spring and summer of 2020 were outright cancelled, but some managed to revise their format and be held virtually later in the year. This was achieved with a combination of live-streaming and pre-recorded content, all of which became on-demand during the conference. Viewers could ask questions through a chat function, or by posting questions directly to the presentation page. While early attempts to host large virtual meetings with researchers in multiple time zones faced a steep learning curve, overall, I think many people realized the potential provided by a virtual platform. For example, without travel costs, more students and early career researchers could afford to attend, and researchers with family care, health, or other constraints could participate on their own time.

Seven of the eight planned scientific presentations of my work took place in 2020, listed here with some links to video content.

Outreach

Screenshot from an online seminar. The video of the speaker is in the upper right corner, and the title slide is the rest of the image. The seminar is "A crash course in the gut microbiome" by Sue Ishaq at the University of Maine.

Similarly, seven of the eight planned public presentations took place, with some links to video content in the list below:

  1. University of Maine Medicine seminar series (virtual), “A crash course in the gut microbiome” , Nov 6, 2020. pdf of slides with annotated comments: ishaq-ummed-gut-crash-course-20201106
  2. Genomes to Phenomes (G2P) group, University of Maine. Co-hosted a session with grad student Alice Hotopp, on gut microbes and survival of reintroduced animals. Oct 30, 2020.
  3. University of Maine Cooperative Extension Oxford County 4-H Teen Science Cafe (virtual), “Gut microbes on the farm”, Oct 15, 2020. 
  4. BioME (Bioscience Association of Maine) Virtual Coffee Hour, “What is a microbiome and where can I get one?” Oct 14, 2020. I introduced myself and my research to 65 participants, who are biomedical professionals and state representatives in Maine. 
  5. University of Maine Cooperative Extension Oxford County 4-H Jamboree (virtual), “Gut microbes on the farm”, Aug 13, 2020. Video.
  6. Invited to lead Journal Club with the Fogler Library, August 4, 2020. led a 1 hour discussion on gut microbes and survival of reintroduced animals.
  7. Albright College Science Research Institute summer program 2020, which engages grades 5-12 in research.  “A crash course in the gut microbiome”, virtual presentation, Aug 4, 2020.

I’ve also been endeavoring to promote the AVS Capstone Experience projects, in part by sharing student-written project summaries on social media and UMaine news outlets. I will do something similar at the end of the spring 2021 semester when projects are complete. And, the online conferences have gotten me thinking about how to create an on-demand virtual symposium that is open to the public…

Blog

I published 45 posts this year, including this one, and was much chattier this year with over 26,000 words total. The most popular post this year was What is academic Outreach/Extension, a sleeper post from 2017 which finally ended the popularity reign of Work-Life Balance: What Do Professors Do?. A number of posts were tied for the least popular this year with one view each, but at the bottom of that possibly-arbitrary list, was A collaborative project got published on the biogeography of the calf digestive tract!, a publication announcement from 2018.

My site had its most popular year, with just over 5,000 visitors taking >8,250 views from 112 countries, as shown in the image below. This November had a record number of visitors, with >1,100! In total, my site has had >15,200 visitors and just under 24,000 views since January 2016, more than I had imagined possible when I began. The website visitors are joined by 64 wordpress followers, 100 on Instagram, 113 on Facebook, nearly 1200 on Twitter, and 0 on Tumblr, which I set up because wordpress will auto-reblog to there, just in case anyone still uses Tumblr.

Life

I picked up a new hobby this year – axe throwing! I tried it at an axe bar last winter and instantly took a shine to it. We made wood targets at home and bought a few throwing axes, and while I haven’t become the maverick I had hoped, it is a lot of fun. I’ve also picked up an arguably more useful skill, basic electrical work to change outlets and light switches! We’ve been slowly updating and renovating our house, and I’m looking forward to learning drywalling and flooring next near.

Looking Ahead

2021 is anticipated to be an exciting year, and will be a combination of wrapping up current projects so some of my students can graduate, as well as progressing the graduate work of Johanna and Sarah. In my “free time”, I’ll continue to fine-tune my curricula, and it’ll be back to the writing table as I revise the research proposals that I submitted this year which were not awarded funding. Of the twelve proposals I submitted in 2020, two were awarded, one is already revised and back in review, at least two will be revised and resubmitted, and at least two new ones are planned.

I’ll be part of my first graduate thesis defense as part of the committee, as Tindall Ouverson is expected to defend her master’s in 2021 from Montana State University. Tindall’s first paper on soil bacteria in agricultural fields is currently in review, and the data analysis for two more (one of which is not on soil microbes) is underway.

I’ll also be leading the committee for Jade’s Honors thesis defense in March. Alex won’t be giving a defense to finish her degree, but she’ll still be informally meeting her committee to reflect on her academic journey and if she’s prepared for a professional career. Johanna and Sarah will soon be inviting faculty to their committees, and next year I will be chairing those meetings.

I’ll be teaching the AVS 402 Capstone class for the first time, but as I already spent the fall semester with AVS seniors in AVS 401, it shouldn’t be any trouble. Just a LOT of revising papers and giving feedback. I’ll be teaching my DNA analysis class again, and will spend the next few weeks updating the materials from last spring when I taught the special topics version. I’ll also be compiling datasets for my students to work on, and hopefully, to turn into scientific manuscripts by the end of the semester.

A number of events developed by the Microbes and Social Equity working group will come to fruition in 2021, and I will finally be able to tell you about them in detail! Stay tuned for information on a speaker series running from February through April, a hybrid (virtual and in person) symposium in June, and a public announcement of a scientific journal special collection.

I’m also pleased to say that one of my cousins will be joining the website behind-the-scenes in 2021, to add alternative text to my website images to make them more inclusive. This and other work will serve as part of the requirement for science/service hours for membership to the Science National Honor Society! I’ll leave it to my cousin to make a formal introduction in a blog post on science accessibility, but welcome to the team!


See you next year!

Title slide of a presentation on "Framing the discussion of microorganisms as a facet of social equity in human health" by Dr. Suzanne (Sue) Ishaq for the inVIVO Planetary Health 2020 conference.

The year of the virtual conferences

2020 has been an interesting year for scientific conferences and meetings, which typically bring dozens to thousands of researchers and professionals together to share their work. Some of the bigger meetings, or those occurring early on in the pandemic, elected to cancel their events because there was no time to adjust the logistics for hosting a massive meeting online.

As the year progressed with no sign of the pandemic abating, more conferences opted for a modified event online. This included live-stream and/or recorded content, spacing the event over a longer period to reduce “zoom fatigue”, and making network events smaller virtual versions. It certainly would have been more rewarding to be able to have these in person, but I am pleased that conference organizers chose safety as their priority.

In some ways, having virtual content made the material more accessible. recordings meant you could watch content at your convenience, more organizations provided or required subtitles for presentations, and those who would otherwise not be able to attend, because of cost, childcare, or travel constraints, were able to participate.

The Ishaq Lab presentations for 2020 is below, with presenters denoted with an asterisk (*).

  1. Ishaq*, S.L.”Framing the discussion of microorganisms as a facet of social equity in human health”, inVIVO Planetary Health 2020 meeting. (revised to virtual) Amsterdam, Netherlands. Dec 2020.
  2. Yeoman*, C., Lachman, M., Ishaq, S., Olivo, S., Swartz, J., Herrygers, M., Berarddinelli, J.  “Development of Climactic Oral and Rectal Microbiomes Corresponds to Peak Immunoglobin Titers in Lambs.”  Conference of Research Workers in Animal Diseases (CRWAD) 2020. (revised to virtual) Dec 5, 2020.
  3. Ishaq*, S.L., Hotopp, A., Silverbrand, S.,   MacRae, J.,  Stock, S.P.,  Groden, E. “Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?” Entomological Society of America 2020. (revised to virtual). Nov 15-25, 2020.
  4. Ouverson*, L..,  DuPre, M.E., Ishaq, S.L.,  Bourgault, M., Boss, D., Menalled, F., Seipel, T. “Soil microbial community response to cover crop mixtures, termination methods, and climate in the Northern Great Plains.” Ecological Society of America (ESA) 2020. (revised to virtual) Salt Lake City, UT. Aug 2020.
  5. Menalled*, F.D., Seipel, T., Ishaq, S.L. “Agroecosystem resilience is modified by management system via plant–soil feedbacks.” Ecological Society of America (ESA) 2020. (revised to virtual) Salt Lake City, UT. Aug 2020.
  6. [meeting cancelled] Horve*, P.F., Dietz, L., Ishaq, S.L., Fretz, M., Van Den Wymelenberg, K. “Characterization of Viable Microbial Communities on Healthcare Associated Window Components.” American Society for Microbiology Microbe 2020, Chicago, IL. Jun 2020.
  7. [meeting cancelled] Horve*, P.F., Dietz, L., Ishaq, S.L., Fretz, M., Van Den Wymelenberg, K. “Characterization of Viable Microbial Communities on Healthcare Associated Window Components.” 2020 Microbiology of the Built Environment (MoBE) Gordon Research Conference, Andover, NH. Jun 2020.
  8. Ishaq*, S.L. “Framing the discussion of microorganisms as a facet of social equity in human health”. 3rd annual  Institute for Health in the Built Environment Build Health 2020. (revised to virtual) Portland, OR. May 2020. (invited). Video.
  9. Zeng*, H., Safratowich, B.D., Liu, Z., Bukowski, M.R., Ishaq, S.L. “Supplementation of calcium and vitamin D reduces colonic inflammation and beta-catenin signaling in C57BL/6 mice fed a western diet.” American Society for Nutrition 2020. (revised to virtual) Seattle, WA. June 2020.
Screenshot from an online seminar. The video of the speaker is in the upper right corner, and the title slide is the rest of the image. The seminar is "A crash course in the gut microbiome" by Sue Ishaq at the University of Maine.

UMaine Institute of Medicine seminar available online

Last Friday, I gave a seminar on “A crash course in the gut microbiome” to the University of Maine Institute of Medicine as part of their fall seminar series. You can find the previous seminars in that series here.

I was delighted to have the opportunity to share my science to researchers around Maine, and to have so many engaging questions!

You can find my seminar recording here, and a pdf of the slides with my presenter notes as annotated comments can be found here:

Woman in a dress sitting in front of a laptop displaying the title slide to a presentation called "Microbes on the Farm".

Virtually speaking

This fall, my speaking engagements will all be held virtually, to aid in ongoing infectious-disease-prevention protocols. While in place to reduce the spread of SARS-CoV-2, these same protocols will also help me avoid the annual fall respiratory infection that I otherwise inevitably encounter while working with overly-stressed students.

But, staying away from others doesn’t mean I can’t stay connected! Virtual events might not feel as fun, but they have allowed me to reach a wider audience, because recorded talks are made available after the live event. And, annotated or subtitled recordings make my talks more accessible!

This fall, I have several public talks and scientific presentations lined up:

  1. University of Maine Cooperative Extension Oxford County 4-H Teen Science Cafe (virtual), “Gut microbes on the farm”, Oct 15, 2020. For teens, this event is free but does require registration to obtain the link.
  2. BioME (Bioscience Association of Maine) Virtual Coffee Hour, Oct 14, 2020. This event is open to the public but requires registration.
  3. Genomes to Phenomes (G2P) group, University of Maine. Co-hosting a session with grad student Alice Hotopp, on gut microbes and survival of reintroduced animals. Oct 30, 2020. Link available to University of Maine community members.
  4. University of Maine Medicine seminar series (virtual), “A crash course in the gut microbiome” , Nov 6, 2020. This event is open to the public and free, but does require registration to obtain the link.
  5. Hotopp, A., Silverbrand, S., Ishaq, S.L.,  MacRae, J.,  Stock, S.P.,  Groden, E. “Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?” Entomological Society of America 2020 (virtual). Nov 15-18, 2020. This pre-recorded seminar requires paid event registration.
  6. Yeoman (presenter), C., Lachman, M., Ishaq, S., Olivo, S., Swartz, J., Herrygers, M., Berarddinelli, J.  “Development of Climactic Oral and Rectal Microbiomes Corresponds to Peak Immunoglobin Titers in Lambs.”  Conference of Research Workers in Animal Diseases (CRWAD) 2020. (Virtual) Dec 5, 2020. This seminar requires paid event registration.

Still time to sign up for UMaine 4H virtual summer programs!

Looking for kids’ activities for the summer? Check out the virtual programs hosted by the University of Maine Extension 4H! Learn about animals, how to care for them, and how your food system works.

From their main page, you can find descriptions of each virtual session, including subject material, presenter, and recommended age group (k-12). You can register for as many or as few sessions as you like, which will be delivered over Zoom.

Registration is free! But if you are able to donate to support the program, those are welcome through the 4H site.

I’ll be presenting on Thursday, August 13th, 2020 at 3 pm EST.

Gut Microbes on the Farm

Learn about different digestive tracts in livestock, and the community of microbes living there that help animals digest food, or stay healthy. This presentation will give some background on different digestive tract anatomy, the factors which influence microbes in the gut, and how we can care for animals by caring for their microbes. This presentation will also feature a short presentation on Dr. Ishaq’s journey into science and a Q&A session where attendees can ask questions about gut microbes, life as a scientist, or how to get involved in this time of career. Register by August 12.

Youth ages 12 & up; open to all youth.

Woman with yellow background in a video meeting.

Microbes and Social Equity presentation at IHBE Build Health 2020 virtual meeting

I presented at my first virtual conference; the Institute for Health in the Built Environment Build Health 2020 industry consortium meeting on May 14, 2020.

Comprised of the Biology and the Built Environment Centerthe Energy Studies in Buildings Laboratory, and Baker Lighting Lab, IHBE connects researchers, practitioners, and designers engaged in creating healthier buildings. For the past few years they have hosted a mini-conference in Portland, Oregon in May, but this year a virtual format was a safer choice.

IHBE meeting organizers did a fantastic job at facilitating a remote meeting with a dozen speakers across multiple time zones. This included creating formatted slide decks for speakers to populate, coordinating sections by colors and symbols and providing respective virtual backgrounds for section speakers to use, and use of breakout rooms for smaller discussion groups.

I presented “Framing the discussion of microorganisms as a facet of social equity in human health“, and you can find a recorded version of the presentation here. There are no closed captions, but you can read the audio as annotations here:

The concept of “microbes and social equity” is one I’ve been playing with for a little over a year, and has developed into a colloquium course at the University of Oregon in 2019, an essay in PLoS Biology in 2019, and a consortium of researchers participating in “microbes and social equity part 2”. The Part 2 group has been developing some exciting research events planned for later in 2020, and those details will be forthcoming!

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.

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

Ciencia y aventura en mexico

For the past four days, I have been in Monterrey, Mexico, where I have been fostering international scientific relations in meetings and in the mountains.  It was my very first trip to Mexico, and it was an amazing experience.

After arriving in Monterrey, I was greeted by a research friend of mine, Dr. Jose Garcia-Mazcorro.  We met a few years ago when Jose emailed me to ask questions about a recently published paper on Saccharomyces probiotic treatment in cattle, and our conversations on the ecological theory behind probiotics led to a review paper on the subject, led by Jose and I. It wasn’t until last August when Jose and I actually met in person, at the ISME conference in Leipzig, Germany.

At dinner, I had the opportunity to meet Jose’s wife, Alecia, who is also a researcher, and their son, and discuss everything from aflatoxin to Stephen King’s “It” (we discovered that their son and I were both reading It when I discussed living in Maine, not far from Derry).

The next day, I woke up at 3:45 am to travel to the mountains for an incredible experience: a small-group tour in Matacanes canyon led by Daniel, a mountaineer with 20 years of experience and owner of Todo Avetura. He and Omar, another guide, led us for 12 hours and taught us about Matacanes canyon while we trekked 13 kilometers (8.7 miles) down waterfalls, through caves, over boulders, and over cliffs. Even the drive into and out of the canyon was an adventure; the steep road into the mountains fords rivers and winds along cliff faces.  In the canyon, I got to do many things for the first time, including rappel down the side of two waterfalls; 27 m (88.6 ft) and 15 m (49.2 ft) into a cave, swim through the absolute dark of a river cave system, and jump off of several cliffs into the water below, including a 9.5 meter (31 ft) jump!  It was supposed to be 10 meters, but that looked just a little too terrifying to try so I chose a spot that looked friendlier.  Turns out that jumping 9.5 meters is a lot like getting up to present in front of a large audience, you just have to get up there and do it before you have time to think about and psych yourself out.

The guides were really passionate about the mountains, and they were particular about safety and not rushing or pushing us to the point where we would get hurt.  If you have the chance, and the cohones, to go to Matacanes, I highly recommend Todo Aventura.

On Monday, sore but no worse for wear, I gingerly toured some of the facilities where Jose is currently working, MNA, an animal nutrition company.  I met with company president and nutritionist Dr. Jorge Kawas, and Jose, Jorge, and I discussed the role of microbes in animal nutrition and health. 

Dr. Jose Garcia-Mazcorro and I at MNA in Monterrey.

Monday night, I got to chat one-on-one with Professor T.J. Nagaraja, an author on the Saccharomyces review and a prominent researcher in rumen acidosis, cattle health, and infectious disease. 

The main reason for my trip to Monterrey was to attend and speak at the XXII UANL-Engorda de Bovinos en Corral Symposium.  I presented the opening seminar titled “Raising feedlot cattle with good microbes in mind” (“Cria y engorda de ganado con buenos microbios en mente”).  The video can be found here, and slides with presentation notes here:

Organized by MNA and UANL, the university in Monterrey, the symposium brings together researchers, producers, animal industry professionals, and students to discuss animal health in feedlot cattle.  I was honored to give the opening talk, which will be available online soon, and pleased to hear that the audience did in fact like microbes more than before my seminar!  Usually when I start talking about the gut microbiome people have the urge to run off and wash their hands…

Unfortunately, I had to jump back on a plane shortly after my talk, as I am heading to give a different presentation at the Wildlife Society meeting in Reno, Nevada tomorrow! But, I have plenty of memories and new project ideas to remember my trip by, and hopefully I will come back to Monterrey soon!

OMSI After Dark Presentation on the gut microbiome

Last night I participated in the Oregon Museum of Science and Industry (OMSI) After Dark event: “It’s Alive! (Mind and Body)”.  OMSI regularly puts on After Dark events, where adults can check out the museum, listen to lectures in the planetarium, and engage in interactive science experiments and activities, all while enjoying an open bar.  Last night, I had a great time giving a short presentation on “Ishaq OMSI After Dark 20180425“!

This slideshow requires JavaScript.

Photo Credits: Lee Warren