Team

The Ishaq Lab had its first and second graduate student thesis defense this summer, with Sarah Hosler and Johanna Holman passing their defenses in the same week! They both gave hour-long presentations of their work, answered difficult questions from their committees for another hour, and published all their work to date as a thesis. Johanna’s master’s focused on “Prevention of Inflammatory Bowel Disease by Broccoli-sourced and Microbially-produced Bioactives“, and she has continued with Yanyan Li and I to do her PhD on this. Sarah’s thesis was broader; “Weaving an Interdisciplinary Microbiome Career Using Threads From Different Ecosystems“, and she has taken a job at her undergraduate institution coordinating science education and lab experience for high school students. All of the work from their theses is being written up into manuscripts. Johanna’s literature review was recently published, and will have her other two chapters in review soon, discussed more below. Sarah’s literature review is in review, and her chapters are being added to in preparation for submission to review in early 2023.

Early in 2022, two graduate students joined the Ishaq Lab. Lola Holcomb is a PhD student in the Graduate School of Biomedical Science and Engineering, is based in Portland as GSBSE hosts remote students around Maine. Lola has been focusing on data analysis to understand microbes, health, and social equity. She began first as a rotation student for 10 weeks, and it was such a good match that we promptly assigned her to my lab for the next 4-ish years. Ayodeji Olaniyi is a MS student in Animal Science, and has been assisting on several projects to gain lab experience. He most recently has taken over the scallop tank bacterial culturing project this fall for which we have been processing 150 bacterial isolates through over a dozen culturing tests, which results in hundreds of plates and tubes to make, process, and clean every week for the past two months! There has been a team of undergraduates helping us on this project, discussed more below.

The Ishaq Lab has also been host to two visiting researchers who have been cross-training on our protocols while performing their own research. Dr. Alaa Rabee has been visiting for the last six months on a fellowship from the Cultural Affairs and Missions Sector and Ministry of Higher Education and Scientific Research of Egypt, to study fibrolytic microbes from animals and how the microbes could be used to digest plant biomass for energy production. Dr. Gloria Adjapong is a postdoctoral researcher at the UMaine Cooperative Extension Veterinary Diagnostics Laboratory on a two year fellowship, and has been generously lending a hand in the lab to help us with >700 DNA extractions and sequencing library preparations to investigate bacterial communities in scallop hatcheries.

This year, the Ishaq lab said hello as well as good-bye to students, as we have been around long enough that students are matriculating (graduating) out and moving on to the next stage of their life. Sarah Hosler defended her master’s thesis and is currently developing and hosting high school research programs at Albright College. Undergraduates Rebecca French, Morgan Rocks, Natalie Sullivan, Sophia S., and Izzy S. graduated in May and went on to vet school, lab research, animal medical care, and more. Ellie Pelletier is graduating in May, but has completed her research project and all but one of her courses early so we are counting her as outgoing.

Publications

1. Ishaq, S.L., Turner, S.M., Lee¹, G., Tudor, M.S., MacRae, J.D., Hamlin, H., Bouchard, D. 2022. Warmer water temperature and epizootic shell disease reduces diversity but increases cultivability of bacteria on the shells of American Lobster (Homarus americanus). In review, preprint available.
2. Hosler², S., Kamath, P.L., Ishaq, S.L. 2022.  A review of technological advances and gaps in detecting and understanding Cryptosporidium protozoan parasites in ruminant livestock. In review.
3. Four more are on the cusp of submission for review!

1. Holman², J., Hurd, M., Moses, P.,  Mawe, G.,  Zhang, T., Ishaq*, S.L., Li*, Y. 2022. Interplay of Broccoli/Broccoli Sprout Bioactives with Gut Microbiota in Reducing Inflammation in Inflammatory Bowel Diseases. Journal of Nutritional Biochemistry. * contributed equally
2. Ouverson², T., Boss, D., Eberly, J., Seipel, T.,  Menalled, F.D., Ishaq, S.L. 2022. Soil  bacterial community response to cover crops, cover crop termination, and predicted climate conditions in a dryland cropping system. Frontiers in Sustainable Food Systems. 911199.
3. Ishaq, S.L., Wissel², E.F., Wolf, P.G., Grieneisen, L., Eggleston, E.M., Mhuireach, G., Friedman, M., Lichtenwalner, A., Otero Machuca, J.,  Weatherford Darling, K.,  Pearson, A., Wertheim, F.S., Johnson, A.J., Hodges, L., Young, S., Nielsen, C.C., Kozyrskyj, A.L.,  MacRae, J.D., McKenna Myers, E., Kozik, A.J., Tussing-Humphreys, L.M., Trujillo, M., Daniel, G.A., Kramer, M.R., Donovan, S.M., Arshad ¹, M., Balkan¹, J., Hosler², S. 2022. Designing the Microbes and Social Equity Symposium, a novel interdisciplinary virtual research conference based on achieving group-directed outputs. Challenges, 13(2), 30.
   • Invited contribution to Challenges, the journal for the inVIVO Planetary Health research group.
4. Sepiel, T. Ishaq, S.L., Larson, C., Menalled, F. 2022. Weed communities in winter wheat: responses to cropping systems and predicted warmer and drier climate conditions.  Sustainability 14(11), 6880.
5. Ishaq, S.L., Turner, S.M., Tudor, M.S., MacRae, J.D., Hamlin, H., Kilchenmann, J., Lee¹, G., Bouchard, D. 2022. Many questions remain unanswered about the role of microbial transmission in epizootic shell disease in American lobsters (Homarus americanus). Frontiers in Microbiology 13: 824950.
   • Invited contribution to special collection: The Role of Dispersal and Transmission in Structuring Microbial Communities
   • This is the first all-female author team I have published with.
6. Rabee, A.E., Sayed Alahl, A.A., Lamara, M., Ishaq, S.L. 2022. Fibrolytic rumen bacteria of camel and sheep and their applications in the bioconversion of barley straw to soluble sugars for biofuel production. PLoS ONE 17(1): e0262304. 
   • Impact 3.24.
   • Dr. Rabee will be joining my lab as a Visiting Research in 2022.
7. Robinson, J.M., Redvers, N., Camargo, A., Bosch, C.A., Breed, M.F., Brenner, L.A., Carney, M.A., Chauhan, A., Dasari, M., Dietz, L.G., Friedman, M., Grieneisen, L., Hoisington, A.J., Horve, P.F., Hunter, A., Jech, S., Jorgensen, A., Lowry, C.A., Man, I., Mhuireach, G., Navarro-Pérez, E., Ritchie, E.G., Stewart, J.D., Watkins, H., Weinstein, P., and Ishaq, S.L. 2022. Twenty important research questions in microbial exposure and social equity. mSystems 7(1): e01240-21. 
   • Invited to Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure

Editorials published

1. Ishaq, S., and Gilbert, J. Introducing the “Microbiomes and Social Equity” Special Collection. mSystems Aug 29, 2022.

Presentations

The Ishaq lab and our collaborators gave in-person and virtual presentations this year to scientific audiences, to students and faculty as guest seminars, and as media/news interviews. Students Sarah Hosler, Johanna Holman, Lola Holcomb, Alice Hotopp, Alexis Kirkendall Rebecca French, and Ellie Pelletier gave or contributed to presentations in 2022.

1. Kirkendall¹*, A., Ishaq, S. Taking on Multiple Research Projects in a NSF Research Experience for Undergraduates (REU) Summer Program as a Disabled Undergraduate Student. Annual Biomedical Research Conference For Minoritized Scientists (ABRCMS) annual meeting, Anaheim, CA, November 9-12, 2022.
2. Hotopp*², A., Ishaq, S., Frey, S., King, B., Kinnison, M., Kovach, A., Olsen, B., Cammen, K. 2022. Microbial communities of tidal marsh sparrow plumage. Association of Field Ornithologists conference, Plymouth, MA, October 17 – 21, 2022.
3. Wissel*², E., Holman*², J., Hosler*², S., Ishaq, S. Microbes and Social Equity: what is it and how do we do it? Part of Track Hub: ‘Field Work & DEI Part 1: Fostering Equitable Partnerships with the Communities in Your Field Work Location’. American Society for Microbiology (ASM) Microbe 2022, Washington, DC (USA), June 9-13, 2022.
4. Holman, J. M., S. Ishaq, Y. Li, T. Zhang, G. Mawe, L. Colucci, J. Balkan. Prevention of Inflammatory Bowel Disease by Broccoli Sourced and Microbially Produced Bioactives.  American Society for Microbiology (ASM) Microbe 2022, Washington, DC (USA), June 12, 2022.
5. Hosler²*, S., Grey, E., Dankwa, A., Perry, J., Bowden, T., Beal, B., Ishaq, S. Initial descriptions of  the microbes of farmed Atlantic sea scallop (Placopecten magellanicus) veligers and rearing tanks. American Society for Microbiology Microbe 2022 meeting. Washington, D.C.. June 9-13, 2022.
6. Hosler²*, S., Grey, E., Ishaq, S. Comparing the microbiome of wild and farmed Atlantic sea scallop (Placopecten magellanicus) veligers. Northeast Aquaculture Conference & Exposition (NACE) and the 41st Milford Aquaculture Seminar (MAS). Portland, Maine. POSTPONED to April 27-28, 2022
7. Ishaq, S., Li, Y., Holman*², J., Zhang, T., Chen, G. “Biogeography may be key to microbial anti inflammatory production using dietary precursors.” Maine Biological and Medical Sciences Symposium, Bar Harbor, ME, April 22-23, 2022. (invited, canceled due to time conflict, graduate student presented in my place)
8. French¹*, R., Beale, J., Ishaq, S. Abstract 0402. Climate Change Affects Wild Mammal Ranges and Health; Will That Also Affect Infectious Disease Exposure Risk at Maine Farms? UMaine Student Symposium (virtual presentation). April 15, 2022.
9. Holcomb²*, Coffman, J., Harrison, B., Tucker, K., Ishaq, S. Abstract 1080. An Overview of Three Biomedical Science Projects across Three Research Institutes. UMaine Student Symposium (virtual presentation). April 15, 2022.
10. Hosler²*, S., Grey, E., Dankwa, A., Perry, J., Bowden, T., Beal, B., Ishaq, S. Abstract 0816. Initial descriptions of the microbes of farmed Atlantic sea scallop (Placopecten magellanicus) veligers and rearing tanks. UMaine Student Symposium (virtual presentation). April 15, 2022.
11. Pelletier¹*, E., Taylor, T., Ishaq, S. Abstract 830. Assessing the Veterinary Needs of Rural Maine and Implementing an Effective Management Plan. UMaine Student Symposium (poster presentation). April 15, 2022.
12. Ishaq, S. “Microbes at the nexus of environmental, biological, and social research.” Iowa State University Spring Microbiology Graduate Student Organization retreat. (virtual). April 14, 2022 (invited co-plenary).
13. Ishaq*, S., Li, Y., Holman², J., Zhang, T., Mawe, G., Hurd, M., Lavoie, B. Baudewyns¹, D., Colucci¹, L., Balkan¹, J., Chen, G, Moses, P. “Biogeography may be key to microbial anti inflammatory production using dietary precursors.”  Congress of Gastrointestinal Function (CGIF), virtual. April 11 – 13, 2022.
14. Ishaq*, S., Li, Y., Holman², J., Zhang, T., Mawe, G., Hurd, M., Lavoie, B. Baudewyns¹, D., Colucci¹, L., Balkan¹, J., Chen, G, Moses, P. “Biogeography may be key to microbial anti inflammatory production using dietary precursors.”  Dartmouth Molecular Microbiology and Pathogenesis (M2P2), February 24 – 25, 2022. (invited)
15. Ishaq, S. ​”Microbes at the nexus of environmental, biological, and social research.” 2nd Rhode Island Microbiome Symposium, virtual, University of Rhode Island Kingston, RI, January 14, 2022. (invited plenary)
16. Ishaq, S. “Moose rumen microbes and you.” The Wildlife Society Nutritional Ecology Working Group Webinar series, (virtual), March 9, 2022.
17. Ishaq, S. “Microbes at the nexus of environmental, biological, and social research” The Microbes and Social Equity 2022 speaker series, virtual, University of Maine and the Microbes and Social Equity working group. January 19, 2022.

Media Interviews

1. “Can broccoli sprouts be used to treat IBD? UMaine researchers investigate”, Carly D’Eon, News Center Maine, Nov 22, 2022.
2. “UMaine researchers studying whether broccoli sprouts can help prevent and treat inflammatory bowel disease”, Marcus Wolf, UMaine News.
3. “Egyptian scientist visits UMaine“, Alaa Rabee and Sue Ishaq, interview by Matthew Jaroncyk, Fox 22 Bangor, Jun 27, 2022.
4. Featured as a woman in microbiome science for Women’s History Month by the National Microbiome Data Collaborative, Twitter, Mar 30, 2022
5. Interviewed for “Invisible Friends”, Dr. Jake Robinson, book in production, 2022.

Research

This year has seen varied topics come through the lab, and there’s too much to include here, but I encourage you to check through the Blog page to find older research posts which provide updates. These and other projects have been successful thanks to hard work and dedication from students and collaborators.

We are also continuing our collaborative investigations into the gut microbiome related to Inflammatory Bowel Disease using mouse models, looking at how dietary components can be used by gut microbes to produce anti-inflammatory compounds that can help the host reduce the symptoms of colitis. In December 2020 and January 2021, we (Drs. Yanyan Li and Tao Zhang and I) ran a mouse trial that generated hundreds of samples, and we have been processing them all year! Over the fall in 2021, our collaborators at the University of Vermont (Dr. Gary Mawe, Molly Hurd, Brigitte Lavoie) ran two more small mouse trials to test some exciting new things. We are days away from submitting both of these for review at a scientific journal.

We are also preparing to run a small pilot project in 2023 looking at broccoli sprout diets in humans, as well as follow up with previously isolated bacteria from mice. We’ll need to screen over 800 bacteria for certain enzyme capabilities and usefulness in producing anti-inflammatories. And, we received funding to continue our investigations into how location in the gut, age, and cooking preparation affects the interaction between diet, gut microbes, and host health! Marissa Kinney will be joining #TeamBroccoli as a Master’s of Science student in Microbiology soon, to help us with all these exciting projects.

In 2021, a pilot study got funded to begin collaborative research with a team at UMaine (Drs. Erin Grey, Jen Perry, Tim Bowden) and the Downeast Institute (Dr. Brian Beal). We collected a few hundred samples from scallops and the biofilms growing in hatchery tanks. Over this year, we have been processing the bacterial community sequencing data and hope to submit a manuscript for peer review and publication soon. This fall, we spent several months processing 115 bacterial isolates through >1800 plates and tubes, thanks to a lot of work from students Ayodeji Olaniyi, Sydney Shair, Keagan Rice, and Lacy Mayo who put in hours and hours leading the efforts on this. We are also grateful to Alaa Rabee, Aaron Williams, Lily Robbins, Ash VanNorwick, and Rebecca Kreeger who provided assistance with media making, inoculating, and the large amount of cleanup (we used glass or autoclavable plastic where possible, and sterilized some single-use plastics to be used as training tools for student education). We were also assisted by Bryanna Dube, who is working on creating outreach/education materials based on our results.

Microbes and Social Equity

The Microbes and Social Equity working group turned 3 years old in December, and is currently at >170 members plus ~100 newsletter subscribers (you can join either list here)! We grew so much that in 2022 that we wrote a separate end of year summary for the group, which will be published soon.

Teaching

This was a busy year for teaching, as I teach 2 courses in the fall and 2 in the spring, which total ~180 students per year. This year, to accommodate disruptions to student schedules over the past few years, I also taught a handful of independent study versions of the Capstone courses for students who could not fit them into their schedule in the recommended semesters. These are considered part of my assigned workload since I taught students who otherwise would have taken this with me during a scheduled course offering, but they did add to my long list of demands for my time this year. There is too much material on my teaching to go into detail here, but I recommend checking out my previous posts on listening to your microbes (a creative assignment), responsible conduct of research (something I integrated into coursework), moving to suggested deadlines, choosing a graduate school, and how departments decide on their curricula.

Website and social media stats

The website gained a phenomenal amount of traffic this year, largely due to MSE, and with just a few days left in the year we clocked nearly 12,500 visitors and nearly 25,000 views!

We had visitors from 125 countries around the globe, with the top 10 listed in the graphic below!

Looking ahead to 2023

The Ishaq Lab has several major projects lined up for 2023, including a broccoli sprout diet pilot project with volunteers from the Bangor area, screening >800 bacteria for their ability to produce anti-inflammatories which we isolated from a mouse study using the broccoli sprout diet, investigating how the age of mice alters the effectiveness of the broccoli sprout diet, identifying 150 bacteria isolated from scallop hatchery tanks, and using >700 DNA samples collected from scallop tanks over a 3 month period to investigate what happens to the bacterial communities in tanks during a larvae rearing trial.

This past year, I was busier than I expected to be, in part because pandemic disruptions began to manifest in students needing much more time with advising to sort out their schedules within tight time constraints with fewer course overrings to choose from, and from faculty and staff taking the early retirement incentive from UMaine to reduce budget deficits which shifted their workload to remaining faculty. This is in addition to the ongoing supply shortages and delays that we are all still facing, which causes disruptions to project timelines and makes sorting out annual budgets that much more time consuming. But, I also had a few extra pilot projects or side projects running, which require more effort and communications in the early stages to get things moving.

Collectively, my workload in 2022 far exceeded what I should be taking on, and I had to set firmer limits on requests for my time, turn down opportunities, and catch up on work during my personal time to an excessive degree. In giving a talk to undergraduates in STEM fields, I urged them to build skills in time management, scheduling in advance, learning when they are able to say no (which is less frequent than you would think), and learning how to prioritize activities when they are unable to say no to requests for their time. My advice to them was that if you are forced to work during your personal time, then you should be working on the activities which benefit you the most. This is particularly important in academia where no matter how many hours I work, I can’t earn bonuses or renegotiate my planned salary increases, but yet there is an ever-increasing need for more productivity and effort. Thus, when I have been working overtime I selected activities which benefit me in other ways, and usually takes the form of writing manuscripts (which I enjoy), proposals (a Sisyphean but necessary task), or blog posts.

In support of healthy restraints on my working hours, I will have to continue to limit requests for my time in 2023 to those which build on my existing directions of teaching and research. Unfortunately, this means turning down many potential collaborations in completely new areas of research for me, to facilitate my focus on the wealth of research and teaching I currently have which fill my days (and weekends) with novelty, surprise, and joy.

Happy New Year!!