I'm an assistant professor of animal and veterinary studies at the University of Maine, Orono, studying how animals get their microbes. I am also the Founder and Lead of the Microbes and Social Equity working group.
The Microbes and Social Equity Speaker Series is back for its third year, starting in just two weeks! We are still finalizing the speaker lineup and the details, but registration is open!
In 2023, we’ll be mixing up the lineup by featuring speakers on a related theme for a few weeks in a row, then inviting them back for a panel discussion. Please note, the talks may be recorded but the panel discussions will not be.
Spring 2023; January 18 – May, Wednesdays from 11:00 AM – 12:00 PM EST.
Dr. Li is an Assistant Professor at the University of Maine. She received her PhD degree in Nutrition and Food Science from Ohio State University. She has been dedicating herself to studying the mechanisms of diet-derived bioactives in protecting against disease process and harnessing the gained knowledge to develop dietary approaches for disease prevention and management for more than a decade. Since 2016, she has been focusing on the interactions between dietary components, in particular glucosinolates from cruciferous vegetables such as broccoli and broccoli sprouts, and gut microbiota, aiming to develop a combined approach for inflammatory bowel disease. Her current research projects are funded by NIH/NIDDK, USDA/NIFA AFRI Foundational Program, and nutrition research programs of private foundations.
Added by Sue: For the past few years, Yanyan and her colleagues have also included the Ishaq Lab, and has led to a rewarding and productive collaboration which has resulted in several recent and forthcoming publications, funding awards, and students trained.
Dr. Sean Gibbons is an Associate Professor at the Institute for Systems Biology, a non-profit research consortium. His lab develops computational and experimental tools for exploring and manipulating host-microbe systems.
Added by Sue: The work from Sean’s group and collaborators has been reshaping the way that host microbial researchers approach their work, by revealing trends through large metanalyses and novel perspectives on using data. Their most recent work has evaluated host-microbial interactions, metabolites, and health.
For the last three years, Sean’s lab has hosted the ISB Virtual Microbiome Series, which is freely available and attracts several thousand participants. The series includes a two day workshop that teaches data analysis skills, and a day-long symposium featuring discussions of current discoveries and conceptualizes the future of microbiome research.
Finally, Sean and his research group have been making science a more welcoming and inclusive place.
Panel discussion on Gut microbiome, nutrition, and food security
This week, we’ll be bringing all of our Theme 1 speakers back to engage in a panel discussion together on the gut microbiome. Panel will be hosted by Sue Ishaq.
Please note, this session will only be featured live in real-time and will not be recorded.
Prenatal to early-life microbes and health
Theme organized by Emily Wissel.
Speaker confirmed but time TBD:
Dr. Eldin Jašarević, Magee-Womens Research Institute, University of Pittsburgh School of Medicine
This week, we’ll be bringing all of our Theme 2 speakers back to engage in a panel discussion together on the microbiome in early life. Panel will be hosted by Emily Wissel.
Please note, this session will only be featured live in real-time and will not be recorded.
The environment, microbes, and us
Anthropology Theme organized by Katherine Daiy and Kieran O’Doherty, and Environmental Theme organized by Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
Speakers confirmed by time TBD:
Dr. Stephanie Schnorr, University of Vienna, “The human-valued interest in microbiome science is the distillation of human-environmental interactions”
Dr. Aminah Al-Attas Bradford, North Carolina State University, “Religion, Race and the Microbe: Theological Analysis of Public Health Resistance in the Pandemicine”
Dr. Anna Krzywoszynska is starting a position as an Associate Professor of Transdisciplinary Human-Environment Relations, Faculty of Humanities, University of Oulu, Finland.
This week, we’ll be bringing all of our Theme 3 speakers back to engage in a panel discussion together on the importance of environmental microbiomes and our place in ecosystems, and then will continue talking about soil health. Panel will be hosted byKatherine Daiy, Kieran O’Doherty, Mallory Choudoir, Mustafa Saifuddin, and Hannah Holland-Moritz.
Please note, this session will only be featured live in real-time and will not be recorded.
The Microbes and Social Equity working group turned 3 years old in December, and we currently have 170 members from around the globe, as well ~100 newsletter-only subscribers (you can join either list here)! MSE continues to grow and shape the future of research, education, and policy thanks to the enthusiasm and support of our members, and we are grateful to have you with us!
We grew so much that in 2022 we added Directors to the Leadership Team, to support our administration and communication needs. In particular, our Directors and other communications specialists helped MSE to improve the way we share information across platforms and within the organization. In 2023, we will continue to improve how members connect with each other, and how people can connect with MSE. Our mailing list is the primary way to reach our members, but we also have public pages on Facebook and Twitter, as well as group pages on LinkedIn and Slack.
Speaker series
Early in 2022, we hosted our second annual spring seminar series, which was organized by Sue Ishaq, Mustafa Saifuddin, Emily Wissel, Melissa Manus, Francisco Parada, and the University of Maine Institute of Medicine. The series had 411 attendees and 901 registrants total across the 14 talks, which is more than the 2021 series had. These and previous talks have been used for teaching materials at several colleges and universities. In case you missed it or want to relive the moments, you can find links to the talks here.
The talks also garnered more attention in the UMaine community this year. Patricia Kaishian’s April 13 talk was promoted as part of the University of Maine Impact Week, and journalist Samantha Sudol of the MaineCampus wrote summaries on talks by Jake Robinson and Patricia Wolf.
Summer symposium
Our symposium in 2022 was a little different than the first version, in that our 5 themed days focused on “Developing transformative research skills”, organized by Sue Ishaq, Ari Kozik, Ashley Toney, Emily Wissel, Kieran O’Doherty, Mallory Choudoir, Mustafa Saifuddin, Erin Eggleston, Carla Bonilla, Monica Trujillo, and Cecile Ferguson (UMaine Institute of Medicine). Our themes this year were “Context-aware experimental designs”, “Blending biological, social, and humanities writing”, “Transforming your research for policy engagement”, “Community engagement and collaboration”, and “MSE Education Practices and Curriculum design”.
This year’s symposium featured 20 speakers across 5 themed days with 3 plenary-style talks/day, followed by 90 min of small-group discussion led by speakers and MSE members. Participants were encouraged to “problem solve” a suggested topic or one of their own choosing to create action items that were meaningful to them, such as ideas for curricula development, identifying research needs or best practices, suggestions for engaging research in policy, and more. The symposium hosted 220 participants (460 registrations) overall and 121 across the breakout room discussions. Registrants were from 23 countries, students and researchers from various fields and career levels, Maine State legislators, and the public. The symposium led to 16 drafted resources documents written by participants.
Special collection of research articles at mSystems
The MSE special collection in the mSystems Journal has published nearly half of the anticipated contributions so far. The inaugural piece was written by a group of MSE members, and has since been joined by 10 other articles and an editorial.
Indigenous knowledge and the microbiome – bridging the disconnect between colonised places, peoples, and the ‘unseen’ influences which shape our health and well-being (Accepted)
MSE held special sessions at two scientific conferences in 2022. At ASM Microbe, Monica Trujillo, Ariangela Kozik, Carla Bonilla, and Sue Ishaq hosted a panel discussion:Microbes and Social Equity: the Microbial Components of Social, Environmental, and Health Justice. The panelists covered many aspects important to MSE from using collaborative, real-life science in microbiology teaching labs, questioning social inequities and disparities in health outcomes, and practicing critical pedagogy in microbiology education using a social equity lens. The panel was highlighted in an article published by ASM and drew an engaged audience eager to learn and share their experiences and vision for microbiology research.
Additionally at ASM Microbe, Emily Wissel, Johanna Holman, and Sarah Hosler were kind enough to give Sue’s presentation on “Microbes and Social Equity: what is it and how do we do it?” for the Field Work and DEI track hub.
Sarah Hosler, Johanna Holman, and Emily Wissel presenting at ASM Microbe.
Sarah Hosler, ASM 2022.
Mallory Choudoir and Naupaka Zimmerman hosted the special session “Adding social contexts to environmental microbiomes” at the 2022 Ecological Society for America meeting in Montreal. A full room gathered to learn about the MSE working group. We drew a diverse crowd (over 40 participants), most were “microbial ecology” graduate students from public research universities, all aiming to learn new information about microbiology and social justice. We held a lively group discussion considering the human dimensions of our research projects and the perceived barriers to broadening our work to explicitly address social and environmental equity. It was fantastic to see so many smiling faces behind masks!
What are we doing in 2023?
In 2023, we will be hosting a speaker series starting in mid January, and this year we will be mixing it up by featuring speakers on a theme for a few weeks and then bringing them back for a panel discussion. We will be sharing the full line-up soon. Also new this year, one link to register them all!
MSE is planning our third annual summer symposium, which is still under development. This will be held virtually, and have a format similar to previous years where we combine plenary talks and discussions. We are hoping to add short talks/posters by students, post docs, and early career researchers this year!
As always, members are encouraged to give presentations or special sessions about MSE at scientific conferences this year, and we have previous session proposals or teaching materials which we can share to facilitate this. We also encourage members to get in touch with MSE with questions about resources, networking, or initiatives you would like to suggest.
MSE is continuing to add the rest of the contributions to the mSystems special collection in the first half of 2023, and as always we are enthusiastic about our members connecting and sparking collaborative projects!
This was year 3 for the Ishaq Lab at UMaine, and we celebrated all of 2022 with new students, new projects, new funding, and exciting results! Here are some highlights, but you can check out previous blog posts in the archives for more detail. As per usual, I have divided the summary into sections: Team, Research, Publications, Presentations, MSE, Teaching, Website, and looking to the year ahead.
Team
Lacy Mayo, Keagan Rice, and Sydney Shairculturing.
Sarah Hosler, Johanna Holman, and Emily Wissel presenting at ASM Microbe.
Gloria Adjapong extracting hundred of DNA samples.
Sydney Shair and Keagan Rice preparing media.
Aaron Williams, Ayodeji Olaniyi, Sydney Shair, and Keagan Rice culturing.
Ayodeji Olaniyi culturing.
Lacy Mayo making media.
Alexis Kirkendall collected samples from calves.
Alexis Kirkendall processing microscope slides.
Sarah Hosler presenting at ASM Microbe.
Ayodeji Olamiyi processing microscope slides.
Sarah Holser is walking in the UMaine 2022 graduate graduation, as she will be defending her master’s of science thesis this summer.
Alexis Kirkendall processing microscope slides.
Sarah Hosler defending her master’s thesis.
Some of the 2021/2022 Ishaq Lab members. From the left: Maria, Sue, Sarah, and Ayodeji.
Johanna Holman beginning her master’s defense presentation.
Sue, Lola Holcomb, and Sarah Hosler hanging out in Portland.
Me on the big screen at ASM Microbe.
Johanna Holman at her ASM Microbe 2022 poster
Some of the 2021/2022 Ishaq Lab members. From the left: Sophia, Isabelle, Rebecca, Morgan, Natalie, and Sue.
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.
My dog, Izzy, has been dutifully coming to campus this fall to attend classes and entertain and calm the students, distract Zoom meetings by trying to climb out the window behind me, and help catalogue all the squirrels on campus.
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
We had a productive year for peer-reviewed journal publications – with 7 published! Several of these have been in development since prior to 2022, several are the first publications for students, and all of which are thanks to my fabulous research collaboration team that now spans the globe. There are a handful more papers in peer review at scientific journals, and others which are in preparation and which we hope to submit for peer review in 2023. Below; 1 undergraduate student I mentored, 2 graduate student I mentored for this project
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.
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.
Four more are on the cusp of submission for review!
Dr. Rabee will be joining my lab as a Visiting Research in 2022.
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. mSystems7(1): e01240-21.
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.
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.
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.
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.
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.
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.
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
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)
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.
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).
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.
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)
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)
Ishaq, S. “Moose rumen microbes and you.” The Wildlife Society Nutritional Ecology Working Group Webinar series, (virtual), March 9, 2022.
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.
Featured as a woman in microbiome science for Women’s History Month by the National Microbiome Data Collaborative, Twitter, Mar 30, 2022
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.
The collaborative work we’ve been doing on broccoli sprouts, gut microbes, and Inflammatory Bowel Disease has had plenty to celebrate this year. In addition to defending her master’s thesis, Johanna authored her first first-authored publication: a review on broccoli anti-inflammatories and current research into how gut microbes can help.
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.
The Ishaq Lab has also been very busy working on projects to investigate how, when, and from where Atlantic sea scallops get their microbes.
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.
Lobster was back on the menu this year as I finished up a data analysis I had been picking away at for two years. This study is available as a preprint (a research article that is currently being peer-reviewed but isn’t finalized yet).
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!
I published a record 82 blog posts, but this included a few dozen that were just promoting events for MSE.
I wrote more than 34,900 words in posts this year!
The page on the 2021 MSE speaker series was the most popular for visitors this year, with MSE symposia and the 2022 series also being popular.
People shared this content on a variety of social media outlets.
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.
Over the past few months, a large team of undergraduate, graduate, and postdoctoral researchers, and I, have been processing hundreds of samples from our scallop hatchery microbiome project. As 2022 winds down, so does the first phase of our lab work, and we are taking a well-deserved break over the holidays before we launch additional lab work, data analysis, and manuscript writing in 2023.
In 2021, the Ishaq Lab, collaborators at UMaine, and collaborators at the Downeast Institute ran a pilot project to investigate the bacteria that associate with sea scallop larvae in hatcheries, and how this is develops in relation to bacteria in hatchery tanks over time. For that project, we collected hundreds of culture plates with a specialized media that selects for certain species of bacteria.
When tanks are drained and cleaned every two days, cotton swabs are rolled across part of the bottom or side of the tank and used to inoculate bacteria onto these culture plates. This is part of a routine screening for pathogens, and don’t worry, we aren’t finding bacteria that causes disease in humans. But, these screening plates creates a useful starting point for our research on bacterial community dynamics.
Tank swab samples are used to inoculate TCBS plates to screen for Vibrio and similar bacteria
We received over 200 of these TCBS culture plates, and from them we isolated 140 bacteria in 2021 and early 2022 which we archived at -80 degrees Celsius. This was part of Sarah Hosler’s master’s of science thesis in August of 2022, and has since been passed to Ayodeji Olaniyi for part of his master’s of science thesis.
This fall, we were able to recover 115 of these isolates from the deep freeze, and tested them on 12 different media in duplicate, which created >1800 cultures plates and tubes, and 230 microscope slides!
This massive undertaking would not have been possible without a large team helping with the lab work, including rockstars 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.
Now, our team will focus on analyzing the results of all these microbiology tests and look for trends. Some will also be heading to the Perry Lab to learn how to perform quantitative polymerase chain reactions (qPCR), in which we use a modified version of DNA replication to count the copies of specific genes. We will use this to look for genes which confirm the identity of our bacteria.
Beginning in summer 2022, the Ishaq Lab has also been part of a state-wide research and commercial collaboration to understand and improve sea scallop production in hatcheries and farms. As part of that project, we received 1500 DNA samples from different hatchery tanks or larvae over the summer/fall rearing season.
Gloria Adjapong is a Postdoctoral Fellow at the UMaine Cooperative Extension Veterinary Diagnostics Lab, and she has been graciously extracting these samples as part of her cross-training in the Ishaq Lab. We will use the extracted DNA to sequence the bacterial communities to identify which bacteria are present, and when, to understand microbial community dynamics over time and in relation to scallop health.
The Ishaq Lab is pleased to welcome Marissa Kinney as a Master’s of Science student in Microbiology, beginning in January 2023! She’ll be joining ‘Team Broccoli‘ to investigate the 806 bacteria we isolated from the digestive tracts of mice eating a broccoli sprout diet, in a previous experiment on broccoli sprouts, microbes, and resolving colitis.
Master of Science student, Microbiology and Animal and Veterinary Sciences
Blurb: Marissa is a Masters student who loves learning and bench microbiology. She completed her undergraduate at the University of Maine in 2021, earning a BS in Microbiology and a BS in Cellular/Molecular Biology. She devoted a large portion of her time in undergrad to research in the laboratories of Dr. Julie Gosse and Dr. Edward Bernard. Since graduating, she worked in the field of public health at UMaine’s Margaret Chase Smith Policy Center, collecting and processing data about violent and drug-related deaths in Maine. While her role at the Center was one she loved dearly, she feels a big pull towards laboratory work and academic research. She recently joined the Ishaq lab and is excited by the new opportunities this position brings.
Congratulations to Dr. Adwoa Dankwa, who defended her doctoral dissertation today on the microbial communities and metabolites in kombucha and kefir!
Adwoa has a background in plant pathology, but she has been working with her adviser, Dr. Jennifer Perry, in the Human Nutrition and Food Sciences program for the last few years on understanding the microbial and chemical composition of fermented non-dairy low alcohol beverages and how these influence consumer acceptability over time.
I’ve been mentoring Adwoa on microbial community data analysis for her project, and look forward to the manuscripts in development from her work. She and I previously published together when she completed the data analysis for a project in my DNA sequencing data analysis class.
Adwoa is beginning a postdoctoral research position in the Perry, and we are all delighted that she’ll continue to be here to brighten our days.
Adwoa originally hails from Ghana, and she generously gave the committee some gifts which were etched with kinds words and symbols from home.
A massive literature review led by Johanna Holman, and featuring our collaborative team of broccoli sprout and microbes researchers, was accepted for publication!
As part of her master’s of science thesis, Johanna Holman reviewed hundreds of journal articles on anti-inflammatory, health-promoting dietary compounds in broccoli and other vegetables or fruits, and how microbes in the digestive tract can transform inactive precursors from foods into those beneficial compounds. This is part of a broader research collaboration on how glucoraphanin in broccoli sprouts can be made into sulforaphane, which acts as an anti-inflammatory in humans. Humans are unable to convert glucoraphanin to sulforaphane, and a small amount of this occurs naturally thanks to enzymes in the broccoli sprouts. But, certain gut microbes can make the conversion and this has helped resolve colitis and other symptoms in mice in laboratory trials (manuscripts in preparation).
Inflammatory Bowel Diseases (IBD) are chronic, reoccurring, and debilitating conditions characterized by inflammation in the gastrointestinal tract, some of which can lead to more systemic complications and can include autoimmune dysfunction, a change in the taxonomic and functional structure of microbial communities in the gut, and complicated burdens in a person’s daily life. Like many diseases based in chronic inflammation, research on IBD has pointed towards a multifactorial origin involving factors of the host’s lifestyle, immune system, associated microbial communities, and environmental conditions. Treatment currently exists only as palliative care, and seeks to disrupt the feedback loop of symptoms by reducing inflammation and allowing as much of a return to homeostasis as possible. Various anti-inflammatory options have been explored, and this review focuses on the use of diet as an alternative means of improving gut health. Specifically, we highlight the connection between the role of sulforaphane from cruciferous vegetables in regulating inflammation and in modifying microbial communities, and to break down the role they play in IBD.
Yanyan Li and I sat down yesterday with Carly D’Eon, a reporter with News Center Maine, to talk about our ongoing research into broccoli sprouts, gut microbes, and Inflammatory Bowel Disease!
It’s been a few years in the making, but our draft manuscript on lobster shell microbes, epizootic shell disease, and climate change is available online as a preprint (not yet peer reviewed)! You can read the preprint here, and the summary is below.
I joined this project back in the summer of 2020, when I was given a large 16S rRNA gene sequence dataset of bacterial communities from the shells of lobsters by a research group at UMaine who had been studying lobster health for some time. My first point of contact on the project was Jean MacRae, an Associate Professor of Civil and Environmental Engineering at UMaine, who had been working on bacterial community sequencing on other projects which I’ve been involved in, and who has been involved with MSE, and this will be our fourth publication together!
Jean introduced me to the original research team, including Debbie Bouchard, who is the Director of the Aquaculture Research Institute and was researching epizootic shell disease in lobsters for her PhD dissertation; Heather Hamlin, Professor and Director of the School of Marine Sciences; Scarlett Tudor, the Education and Outreach Coordinator at the ARI; and Sarah Turner, Scientific Research Specialist at ARI.
I used the data as a training opportunity for Grace Lee, who at the time was an undergraduate at Bowdoin College participating in the abruptly cancelled summer Research Experience for Undergrads program at UMaine in summer 2020. Instead, Grace joined my lab as a remote research assistant and we worked through the data analysis over the summer and fall. Grace has since graduated with her Bachelor’s of Science in Neuroscience, obtained a Master’s of Science at Bowdoin, and is currently a researcher at Boston Children’s Hospital while she is applying to medical school.
Earlier this year, the research team, along with social science Masters student Joelle Kilchenmann, published a perspective/hypothesis piece which explored unanswered questions about how the movement of microbes, lobsters, and climate could affect the spread of epizootic shell disease in lobsters off the coast of Maine.
Suzanne L. Ishaq1,2,, Sarah M. Turner2,3, Grace Lee4,5,M. Scarlett Tudor2,3, Jean D. MacRae6, Heather Hamlin2,7, Deborah Bouchard2,3
1 School of Food and Agriculture; University of Maine; Orono, Maine, 04469; USA.
2 Aquaculture Research Institute; University of Maine; Orono, Maine, 04469; USA.
3 Cooperative Extension; University of Maine; Orono, Maine, 04469; USA.
4 Department of Neuroscience, Bowdoin College, Brunswick, ME 04011; USA.
5 Boston Children’s Hospital, Boston, MA 02115; USA.
6 Department of Civil and Environmental Engineering; University of Maine; Orono, Maine, 04469; USA.
7 School of Marine Sciences; University of Maine; Orono, Maine, 04469; USA.
Summary
The American lobster, Homarus americanus, is an economically valuable and ecologically important crustacean along the North Atlantic coast of North America. Populations in southern locations have declined in recent decades due to increasing ocean temperatures and disease, and these circumstances are progressing northward. We monitored 57 adult female lobsters, healthy and shell-diseased, under three seasonal temperature cycles for a year, to track shell bacterial communities using culturing and 16S rRNA gene sequencing, progression of ESD using visual assessment, and antimicrobial activity of hemolymph. The richness of bacterial taxa present, evenness of abundance, and community similarity between lobsters was affected by water temperature at the time of sampling, water temperature over time based on seasonal temperature regimes, shell disease severity, and molt stage. Several bacteria were prevalent on healthy lobster shells but missing or less abundant on diseased shells, although putative pathogens were found on all shells regardless of health status.
The Ishaq Lab 