Updates

2023 Year in Review

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This was year 4 for the Ishaq Lab at UMaine, and we celebrated all of 2023 with new students (some of whom are mentioned here), new projects, new publications, and exciting results! Here are some highlights, but you can check out previous blog posts in the archives for more detail. As usual, I have divided the summary into sections: Team, Research, Publications, Presentations, MSE, Teaching, Website, and Looking Ahead.

Team

Sue Ishaq, Yanyan Li, and Johanna Holman, pose in various labs where the three research broccoli. Photo Credit: Patrick Wine, UMaine.
Benjamin Hunt

Johanna Holman completed her first year and a half of her PhD, starting when she completed her master’s in August 2022. She’s been managing multiple projects and teams this year, including a large-scale culturing assay of bacteria, a diet study in people, contributing to a literature review on oxidative stress and cruciferous veggies in the diet, leading a literature review on fiber intake and global distribution of inflammatory bowel diseases, and preparing for two large-scale mouse trials in 2024!!

Johanna was lead author on a very exciting publication about feeding steamed broccoli sprouts to young mice which had symptoms similar to ulcerative colitis, as a means of introducing anti-inflammatories into the intestines at the site of inflammation. The steamed sprouts were very effective in mice, especially in certain locations in the gut, which we are currently exploring in more detail. And, she was second author on Lola’s paper which makes two papers published for Johanna this year! Johanna is planning her comprehensive exam early in 2024, after which she’ll be eligible to apply for doctoral fellowships and funding.

Lola Holcomb passed her PhD qualifying exam this year and advanced to candidacy! The exam in the GSBSE program requires students to write a research proposal in the style of an NIH graduate fellowship on a topic which is different from their primary focus, but which uses similar methods or approach to what they have been learning. By requiring a new topic, the dissertation committee can assess a student’s ability to synthesize new information into a plan.

In addition to the written experimental design and accessory documents (about 20 pages), Lola presented her proposal to the committee in an hour-long presentation and then answered questions about experimental design and analysis for both the exam topic and the dissertation research topic. Lola passed easily, because she’s amassed research experiences in her undergraduate and graduate degrees and has a keen mind for bioinformatics. Now that she is a PhD candidate, Lola will proceed with her research into bacterial biogeography in the gut and how it affects human or animal health.

Lola was lead author on a very exciting publication on feeding raw broccoli sprouts to young mice which had symptoms similar to Crohn’s Disease, as a means of introducing anti-inflammatories into the intestines at the site of inflammation in mice where the immune system plays a large role in the progession of the disease. The raw sprouts were very effective in young juvenile mice, but only mildly effective in adolescent mice, which we are currently exploring in more detail. Lola won a travel award from GSBSE to present this research at microbiome conferences in 2024, and she was second author on Johanna’s paper which makes two papers for her this year! She also submitted her first large-scale funding proposal as a principal investigator, fingers crossed that is awarded!

Ayodeji Olaniyi is wrapping up his master’s thesis in Animal Science, and is planning to defend in January before starting a new job as a researcher! He has been working on the scallop tank bacterial culturing project for which we processed 140 bacterial isolates last fall and into this spring. We hope to have a manuscript submitted for publication in early 2024.

There was a team of undergraduates helping us on this project, discussed more below. Ayo won a Graduate Student Research Award for this work at the UMaine Student Symposium, and a 2023 Travel award from the University of Maine Aquaculture Research Institute Rapid Response Fund to present this work at the NACE/MAS conference in January.

Marissa Kinney joined in January for her Master’s of Science in Microbiology, and has been involved in four of the broccoli projects already!! She contributed qPCR data and analysis to both Johanna’s and Lola’s papers, which makes two papers for her this year! She was awarded a One Health and the Environment NRT Fellowship 2023 – 2024 at UMaine, and was recently awarded research support from the Biomedical Association of Maine!!

Marissa has been providing labwork for several projects trying to quantify glucosinolate-metabolism genes in bacteria from the gut of mice and humans, as well as preparing multiple DNA libraries for sequencing. In early 2024, she’ll be an intern at the UMaine DNA Sequencing Facility where she will learn to generate sequencing data, and she’s been learning to perform the complex analysis of this data in my sequencing analysis class this fall. After her internship, Marissa will be running her own lab experiement, as well as helping on Johanna’s mouse trials.

Three graduate students joined the lab during 2023, Hannah Horecka as a master’s student through the Darling Marine Center working on aquatic animal health, as well as two students on #TeamBroccoli, Ashley Reynolds and Tolu Alaba. Ashley Reynolds is a PhD student in Nutrition/Microbiology who has been working on the broccoli sprout diet trial in humans and is learning the microbiology portion to participate in other projects soon.

Headshot for Esther Alaba, PhD Candidate in Biomedical Sciences

Tolu (Esther) Alaba is a PhD candidate in the GSBSE program, and added her considerable expertise in nutrigenomics, and using dietary phenols to reduce oxidative stress and inflammation, to the lab starting in late September. She has been analyzing data on metabolites, metabolomics, and nutritional patterns in mice and humans. Even though she only recently joined the lab, she has already completed a literature review on oxidative stress and cruciferous vegetables in the diet which is currently in review, and she is helping to prepare two other manuscripts!

Alexis Kirkendall rejoined the lab in summer 2023 to work on bacterial isolates for the broccoli projects, and had been working remotely since she first joined the lab in summer 2022 as an REU student. She just completed her bachelor’s degree at Heidelburg College, and she’s rejoined the lab once again as a PhD student in Microbiology!! In addition to helping Johanna with the mouse trials and learning genomics from Marissa, Alexis will be working on understanding some of the enzymatic pathways that bacteria use to turn the inactive compound in broccoli/sprouts into anti-inflammatories.

Benjamin Hunt

Benjamin and Timothy Hunt have been working on several metanalyses and literature reviews on the translatability of mouse studies of Inflammatory Bowel Disease to human health, as well as data analysis for our collaborators at the University of Vermont. They both contributed bioinformatic analysis to both Johanna’s and Lola’s papers, which makes two papers for them this year!

In 2024, they will continue the data analysis on a small project run by our UVM collabotors, as well as continue working on their literature review. They are in the third year of their undergraduate studies, and are planning for medical school next.

Dr. Gloria Adjapong has continued to support the lab as 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. She recently passed a certification exam that will support her research career.

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. We threw her a 10th birthday party in class in April!

Two members of the Ishaq Lab added a “lab trainee” to their family in 2023, and a third lab member will be welcoming a “trainee” in 2024!! We haven’t found any infant-sized lab coats that are certified for the type of work we do, but we will keep shopping 🙂

Publications

A stack of papers facedown on a table.

We had a productive year for peer-reviewed journal publications – with 7 published! Several of these have been in development since prior to 2023, several are the first publications for students, and all of which are thanks to my fabulous research collaboration team that spans the globe. There are a handful more papers in peer review at scientific journals, and others which are in preparation that which we hope to submit for review in 2024. Below in bold; 1 undergraduate student I mentored, 2 graduate student I mentored for this project, some of whom are primarily mentored in other labs.

  1. Hotopp2, A., Oslen, B., Ishaq, S.L., Frey, S., Kovach, A., Kinnison, M., Gigliotti, F., Roeder, M., Cammen, K. 2023. Plumage microbial communities of tidal marsh sparrows. iScience, Accepted 11/17/2023.
    • Alice is a lab affiliate, and is in Kristina Cammen and Brian Olsen’s labs working on swamp sparrow ecology. I contributed mentoring on DNA extraction and library preparation for amplicon sequencing, as well as bioinformatics analysis of the microbial community dataset.
  2. Holcomb2, L., Holman2, J., Hurd, M., Lavoie, B., Colucci1, L., Hunt1, B., Hunt1, T., Kinney2, M., Pathak2, J., Moses, P., Mawe, G.M., Perry, E., Stratigakis, A., Zhang, T., Ishaq, S.L., Li, Y. 2023. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. mSystems: 00688-23.
  3. Brostow, D.P., Donovan, M., Penzenik, M., Stamper, C.E., Spark, T., Lowry, C.A., Ishaq, S.L., Hoisington, A.J., Brenner, L.A. 2023. Food desert residence has limited impact on Veteran fecal microbiome composition: A United States-Veteran Microbiome Project (US-VMP) Study. mSystems: 00717-23.
  4. Ishaq, S.L., Hosler2, S., Dankwa, A., Jekielek, P., Brady, D.C., Grey, E., Haskell, H., Lasley-Rasher, R., Pepperman, K., Perry, J., Beal, B., Bowden, T.J. 2023. Bacterial community trends associated with sea scallop, Placopecten magellanicus, larvae in a hatchery system. Aquaculture Reports 32: 101693.
  5. Holman2, J., Colucci1, L. Baudewyns1, D., Balkan1, J., Hunt1, T., Hunt1, B., Kinney2, M., Holcomb2, L., Stratigakis, A., Chen. G., Moses, P.,  Mawe, G.M.,  Zhang, T., Li, Y., Ishaq, S.L. 2023. Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice. mSystems: 00532-23.
  6. Betiku, O., Yeoman, C., Gaylord, T.G., Ishaq, S., Duff, G., Sealey, W. 2023. Evidence of a Divided Nutritive Function in The Rainbow Trout (Oncorhynchus mykiss) Mid- and Hind-Gut Microbiomes by Whole Shotgun Metagenomic Approach. Aquaculture Reports 30: 101601.
    • This one dates way back to 2016 when I was a postdoc in Carl Yeoman’s lab in Montana! Omalola was a PhD student at the time, and is currently an Assistant Professor in Florida.
  7. Ishaq, S.L., Turner, S.M., Lee1, G., Tudor, M.S., MacRae, J.D., Hamlin, H., Bouchard, D. 2023. Water temperature and disease alters bacterial diversity and cultivability from American Lobster (Homarus americanus) shells. iScience 26(5): 106606.
    • News articles run in Knox County, Maine (in The Courier-Gazette) and Ellsworth, Maine (in the Ellsworth American)
  8. This one was published online in 2022 and got its official citation in early 2023: Holman2, J., Hurd, M., Moses, P.,  Mawe, G.,  Zhang, T., Ishaq*, S.L., Li*, Y. 2023. Interplay of Broccoli/Broccoli Sprout Bioactives with Gut Microbiota in Reducing Inflammation in Inflammatory Bowel Diseases. Journal of Nutritional Biochemistry 113:109238. * authors contributed equally

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 Johanna Holman, Lola Holcomb, Marissa Kinney, Ayodeji Olaniyi, Sydney Shair, and Keagan Rice gave or contributed to presentations in 2023. Undergrads that I mentored for their Capstone also presented at the UMaine Student Symposium, including Zach Inniss, Kurt Jancsy, and Ellie Pelletier.

  1. Holcomb*, L., Holman, J., Hurd, M., Lavoie, B., Colucci, L.,Moses, P., Mawe, G.M., Perry, E., Stratigakis, A., Zhang, T., Ishaq, S.L., Li, Y. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. American Society for Nutrition annual meeting, Boston, MA. July 22-25, 2023.
  2. Holman*, J., Holcomb, L., Colucci, L. Baudewyns, D., Balkan, J., Chen. G., Moses, P.,  Mawe, G.M.,  Zhang, T., Li, Y., Ishaq, S.L. Steamed broccoli sprouts alleviate gut inflammation and retain gut microbiota against DSS-induced dysbiosis. American Society for Nutrition annual meeting, Boston, MA. July 22-25, 2023.
  3. Toney*, A., Wolf, P., Ishaq, S. Broadening Perspectives by Situating Nutrition Education in Broader Social Contexts: A Study Protocol. American Society for Nutrition annual meeting, Boston, MA. July 22-25, 2023. (poster)
  4. Holcomb, L. Early Life Exposure to Broccoli Sprouts Confers Stronger Protection against Enterocolitis Development in an Immunological Mouse Model of Inflammatory Bowel Disease. UMaine Student Symposium, Orono, ME. April 14, 2023.
  5. Kinney, M. Establishing Growth Curve Assays for Bacterial Glucosinolate Metabolism. UMaine Student Symposium, Orono, ME. April 14, 2023.
  6. Shair, S., Rice, K. Assessment of the Association of Sea Scallop Larvae Mortality and Vibrio spp. in Hatchery Systems. UMaine Student Symposium, Orono, ME. April 14, 2023.
  7. Olaniyi, A. Investigating The Activity of Bacteria Isolated from Tank Biofilms in a Hatchery System for Sea Scallops, Placopecten magellanicus, Larvae. UMaine Student Symposium, Orono, ME. April 14, 2023.
  8. Wijayanayake, R. Utilizing Sulforaphane from Broccoli to Treat IBD. UMaine Student Symposium, Orono, ME. April 14, 2023.
  9. Inniss, Z., Jancsy, K. The Veterinary Immersion Plan: An Innovative Solution to Address Non Predictive Barriers to Entering the Field of Veterinary Medicine. UMaine Student Symposium, Orono, ME. April 14, 2023.
  10. Pelletier, E. Assessing the Small Animal Veterinary Needs of Rural Maine and Implementing an Effective Management Plan. UMaine Student Symposium, Orono, ME. April 14, 2023.

I received several invitations to speak this year!

  1. Ishaq, S. 9th Annual Southern California Microbiome Summit. Riverside, CA, September 22, 2023. (invited)
  2. Ishaq, S. “Scallop microbes and sustainable aquaculture: host-microbe dynamics situated in environmental and social context.” Ecological Society of America (ESA) annual meeting. Inspire session: Microbes as Tools to Solve Ecological Problems for All. Portland, OR, August 6-11, 2023. (invited)
  3. Ishaq, S. “Microbes and Social Equity: what is it and how do we do it?” Boston University Microbiome. July 12, 2023. (invited keynote).
  4. Ishaq, S. “Microbes and Social Equity: what is it and how do we do it?” Harvard Chan-NIEHS Center for Environmental Health’s “Environmental Health in Action” colloquium series. Boston, MA, May 10, 2023. (invited)

Research

This year has seen various 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.

A cartoon of three gastrointestinal tracts showing the locations of inflammation in ulcerative colitis, crohn's disease, or healthy tissue. At the bottom are cross-sections showing thickening of the intestinal wall in patients with Crohn's, and ulcers in patients with colitis.

The collaborative work we’ve been doing on broccoli sprouts, gut microbes, and Inflammatory Bowel Disease had plenty to celebrate this year. We published two major research papers, presented across the country, and doubled the size of #TeamBroccoli.

In December 2020 and January 2021, we (Drs. Yanyan Li and Tao Zhang and I) ran a mouse trial that generated hundreds of samples. This year, Johanna has been leading a team of students (Alexis Kirkendall, Lilian Nowak, Aakriti Sharma, and Jaymie Sideaway) on a culturing project to screen hundreds of bacterial isolates that were collected from the gastrointestinal tracts of mice eating broccoli sprouts. We are testing them for their capacity to metabolize different glucosinolates into anti-inflammatory compounds, as well as grow on different media types. In the process, we found that the bacteria we are using as a positive control likes to move from one test well to another when its favorite media is available — but not when glucose is present.

A cartoon of a bacteria eating broccoli and pooping out sulforaphane
Designed by Johanna Holman

We are also running a small pilot project in 2023-2024 looking at broccoli sprout diets in humans, for which we designed a recipe book, stickers, and spent a lot of time revising protocols and instruction materials to make them more user-friendly. Johanna has been leading the project, and this fall, Ashley, Marissa, and Tolu joined the project to add their expertise in community nutrition, qPCR of bacterial genes, and nutrigenomics, respectively.

  • Broccoli sprouts in a tray

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. Last fall and this spring, we spent several months processing ~140 bacterial isolates through >1800 plates and tubes, thanks to a lot of work from students Ayodeji Olaniyi, Sydney Shair, Keagan Rice, and Lacy Mayo, and a few others who dropped in to help.

I went to the Ecological Society of America annual meeting in Portland, OR in August to present some of the companion work to the Vibrio project, on scallop larval rearing tanks and the bacterial communities we found there. That included an unexpected effect of coastal water dynamics and the phase of the moon. That work has recently been published.

Microbes and Social Equity

The Microbes and Social Equity working group turned 4 years old in December, and is currently at >300 members plus ~130 newsletter subscribers (you can join either list here)! We ran a seminar series and a symposium, and continued to add to the special collection in mSystems. You can check out the brand new Microbes and Social Equity working group webpage for their end of 2023 updates, as well as the program-in-development for our 2024 speaker series.

Teaching

This was a busy year for teaching, as I teach 2 courses in the fall and 2 in the spring, which total ~150-180 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 continued to host a phenomenal amount of traffic, once again largely due to MSE, and with just a few days left in the year we clocked nearly 15,000 visitors (the most ever!) and nearly 25,000 views (almost the most ever)!

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

I published 70 blog posts, including this one, but this included a few dozen that were just promoting events for MSE and did not have unique content.

I wrote more than 41,400 words in posts this year, which is more than last year!

Looking ahead to 2024

Projects: The Ishaq Lab has several major projects lined up for 2024, including the ongoing 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 140 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.

Conferences: I’ll be traveling a lot to present my work in 2024, including chatting with the Microbial Matters podcast, hosting a session on scallops and microbes at NACE/MAS in January, presenting the broccoli work to the Microbiology seminar series at Oregon State University in Corvalis, Center for Microbiome Innovation International Microbiome meeting in La Jolla, and the Institute for Systems Biology in Seattle, hosting a session on food sovereignty and the gut microbiome at ISME 2024 in Cape Town, and more!

Leadership: In 2024 I will be starting my three-year term as the At Large Early Career member of the Board of Directors for the American Society for Microbiology, a 36,000-member international organization!

Tenure: I applied for tenure in the fall of 2023, and will hear back about the university’s decision in 2024. I look forward to celebrating my promotion to tenured Associate Professor 🙂

Work-life balance: My workload in 2022 far exceeded what I should be taking on, and in 2023 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 2023, it was still too much – I worked well over 40 hours per week, even during one month in the summer that I was off contract. Despite this, I managed to enforce time off for myself which is critical to scientific progress. As part of this effort, I made it a point to add personal travel days to my work trips, as I traveled to sunny locations and met with incredible friends and colleagues.

  • Two women laughing and posing for a photo in front of a koy pond.
  • Sean Gibbons, Sue, and Jotham Suez posing on rock path in front of bright pink blooming cherry trees at a Japanese Garden.

In support of healthy restraints on my working hours, I will have to continue to limit requests for my time in 2024 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!!

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