Updates

2025 Year in Review

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The Ishaq Lab celebrated 6 years at UMaine this fall, which coincided with my first sabbatical! 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

  • About half the lab and one of our collaborators was able to join us for an end-of year lunch.
  • Tolu Alaba and Sue Ishaq
  • Aaron Williams
  • Mia Poirier
  • Johanna Holman presenting at the 2024 UMaine student research symposium
  • Sue Ishaq and Alexis Kirkendall posing for a photo in a stairwell.
    Sue and Alexis

Lola Holcomb defended her dissertation and graduated with her PhD in Biomedical Science in May 2025! I was there to give her her PhD hood at the graduation ceremony. She was awarded a USDA pre-doctoral fellowship, sadly she had to decline because the delays in federal funding in 2025 resulted in the award notification being delivered after she graduated. She is currently a postdoctoral researcher at the University of New England. Lola continues to collaborate with the lab while we write up the results from her dissertation work for publication in a scientific journal.

Johanna Holman, PhD candidate in the Microbiology program, is preparing to defend her dissertation early in 2026 (announcement forthcoming)! She was, once again, a teaching assistant at UMaine in Biology. In 2025, she added whole genome and RNA transcriptome genetic library preparation and data analysis to her impressive skillset. She presented her work several times this year, and has spent the past few months writing her work into a dissertation that will be converted to scientific manuscripts in spring 2026. She is planning on a postdoctoral research position focused on the gut microbiome and health (announcement in 2026).

Heather Richard passed her comprehensive exam early in 2025, advancing to PhD candidacy in the Ecology and Environmental Sciences program. She was, once again, a teaching assistant at UMaine in Biology. She’s been analyzing sequencing data from hundreds of samples from salt marsh sediments in Maine to understand how microbial communities affect carbon sequestration. She plans to defend her dissertation in summer 2026.

Alexis Kirkendall finished her second year, and advanced to PhD candidacy in the Microbiology Program. She was, once again, a teaching assistant at UMaine in Biology. She has focused on completing lab work related to probiotic development, for which she won a Graduate Student Research Award from the Bioscience Association of Maine!! Over the next year, she’ll focus on testing some of the probiotic candidates we have selected for their ability to reduce inflammation in vivo.

Ashley Reynolds, R.D., and PhD student (she would be a PhD candidate by now if only her committee could coordinate their schedules to hold a comprehensive exam) in Food and Human Nutrition program. This year, Ashley served as the Instructor for my AVS 254 Intro to Animal Microbiomes course while I was on sabbatical. She has been working on a literature review on diet, the gut microbiome, and neuroinflammation, as well as data analysis on fecal microbiome samples from people experiencing migraines.

Five undergrads graduated in May 2025, while four other undergraduates (some of whom are in the group photos above and listed on the Team page) worked in the lab over the summer and fall on various broccoli sprout projects, to complete their Capstone project or Honor’s thesis. Mia Poirier was awarded a CUGR undergraduate research award for her work. Most of those students are co-authors on the forthcoming publications on that work, thanks to the scale of their contribution. Collectively, the undergraduates contributed to a large-scale bacterial culturing project, a comparative gene project, and the administrative/organizational work required to keep a research lab running.

I was awarded sabbatical this fall, which allowed me to focus on revisions to my courses, revising research proposals to seek elusive federal funding, and supporting my students in writing their work into dissertations and publications. The “break” from teaching and advising allowed me to spend more time on research, including work on broccoli and gut microbiome as well as Microbiome Stewardship, administrative work such as leadership duties for the Microbes and Social Equity working group, and participating in research-curation initiatives, such as the creation of a Microbe Specialist group for the IUCN. I’ll write about my sabbatical experience in a separate post in 2026).

I continued the second year of my three-year term as the At-Large Early Career member of the Board of Directors of the American Society for Microbiology, which currently has >38,000 members around the world. I was honored to help with strategic planning to support microbiological sciences on an international scale, as well as defend training opportunities when funding was rescinded. I also started a three-year term as Senior Editor at the scientific journal mSystems.

Publications

We had a quiet year for lab research publications, as some of our manuscripts were delayed in the peer-review process for an entire year. We spent the last half of 2025 writing up all the projects we’ve been working on over the last few years (some projects take several years to complete), so we have a large number in preparation. But, it was an excellent year for conceptual papers and reviews. 1 undergraduate student I mentored, 2 graduate student I mentored

  1. Alaba2, O.A., Ishaq, S.L., Chen, Y-Y., Calderwood, L.,Hao, J., Zhang, Y. 2025. Warming treatments shift the temporal dynamics of diversity and composition of bacteria in wild blueberry soils. Journal of Applied Microbiology.  Accepted.
  2. Farmer, N.M., Benezra, A., Maki, K., Ishaq, S.L., Kozik, A.J. 2025. Prioritizing Precision: Guidelines for the Better Use of Population Descriptors in Human Microbiome Research. mSystems0:e00640-25.
  3. Gilbert, J.A., Azad, M.B., Bäckhed, F., Blaser, M.J., Byndloss, M., Chiu, C., Chu, H., Dugas, L.R., Elinav, E., Gibbons, S.M., Henn, M.R., Ishaq, S.L., Ley, R.E., Lynch, S.V., Segal, E., Spector, T.D., Strandwitz, P., Suez, J., Tropini, C., Whiteson, K., Knight, R. 2025. Clinical translation of microbiome research. Nature Medicine 31, 1099–1113. Impact Factor 58.7. Review paper.
  4. Gilbert, J., Scholz, A., Dominguez-Bello, M.G., Korsten, L., Berg, G., Singh, B., Boetius, A., Wang, F., Greening, C., Wrighton, K., Bordenstein, S., Jansson, J., Lennon, J., Souza, V., Allard, S.M., Thomas, T., Cowan, D., Crowther, T., Nguyen, N., Harper, L., Haraoui, L-P., Ishaq, S., McFall-Ngai, M., Redford, K.H., Peixoto, R. 2025. Safeguarding Microbial Biodiversity: Microbial Conservation Specialist Group (MCSG) within the Species Survival Commission of the International Union for Conservation of Nature (IUCN). Editorial Published in multiple journals simultaneously, including mSystems, Sustainable Microbiology, the ISME Journal, and FEMS Microbial Ecology.
  5. Gilbert, J., Peioto, R., Scholz, A., Dominguez-Bello, M.G., Korsten, L., Berg, G., Singh, B., Boetius, A., Wang, F., Greening, C., Wrighton, K., Bordenstein, S., Jansson, J., Lennon, J., Souza, V., Thomas, T., Cowan, D., Crowther, T., Nguyen, N., Harper, L., Haraoui, L-P., Ishaq, S., Redford, K. 2025. Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity. Nature Microbiology 10:2359–2360. (correspondence)
  6. Sinnott-Armstrong, N., Forsythe, D., Benoit, J.M., Chappell, C.R., Coe, L.S.Y., Rodrigues de Oliveira, B.F., Evans, N., Fagre, A.C., Gilligan, J.M., Hamilton, M., Henneberry, C.M., Ishaq, S.L., Johnston, J.,  Krichilsky, E., Lopez, J.A., McMonigal, L., Ortiz Alvarez de la Campa, M., Rahman, R., Schwartz, N.E., Talluto, L., Taylor, E.J., Vargas-Muñiz, J.M., Weissman, J.L. 2025. Protect transgender scientists. Science 388 (6753):1283-1284 (letter)
  7. Choudoir, M., Ishaq, S., Beiko, R., Silva, D., Allen-Vercoe, E., O’Doherty, K. 2025. The case for microbiome stewardship: What it is and how to get there. mSystems. 0:e00062-25.  (perspective)
  8. Yang, T., Canham, S., Kasthuriarachchi, T., Kirkendall2, A., Rahman, M.A., Bae, S.H., Zhang, T., Ishaq, S.L., Li, Y., Bai, S. Molecular and Functional Characterization of Nanoscale Broccoli Sprout–Derived Exosomes Reveals Surface Markers, miRNAs, and Targeted Anti-Inflammatory Efficacy.  In review.
  9. Athithan, P., Ishaq, S., Vercoe-Allen, E., O’Doherty, K. Microbes first into the life rafts: preserving microbiomes to secure health in degrading ecosystems.  In review.
  10. Lurgio2, A., Webb, A., Spillane,  T., Rzeszowski,  E., Jones, S., Ishaq, S., Becker, T., Kanwit, K., Brady, D.C. 2026. Seasonality of Vibrio parahaemolyticus in the eastern oyster, Crassostrea virginica, along the coast of Maine, USA. In review.
  11. Mastaloudis**, A., Holcomb2**, L., Fahey, J.W., Olson, C,, Nieman, D., Kay, C., O’Donnell, R., Pecorelli, A., Kinney2, M,, Li, Y., Ishaq*, S.L., Valacchi*, G. 2024. Exogenous Myrosinase from Mustard Seed Increases Bioavailability of Sulforaphane from a Glucoraphanin-Rich Broccoli Seed Extract.   In review for over a year. ** co-first author, * co-senior author.
  12. Alaba2, T.E., Zhang, T., Li, Y., Ishaq, S.L. Steamed broccoli sprouts diet alleviates inflammatory bowel disease by increasing anti-inflammatory, antioxidant and gut protective metabolites in an ulcerative colitis mouse model. Back in review after predatory practices by the first journal we submitted to.
  13. Holman2, J.M., Kirkendall2, A.,Holcomb2, L., Hunt1, T., Hunt1, B., Miriam Talalay1, M., Ruff1, A., Aaron Williams1, A., Kasthuriarachchi, T., Li, Y., Ishaq, S.L.  Identification of bacteria that metabolize glucoraphanin to anti-inflammatory metabolites for reducing gut inflammation. In preparation.
  14. Holcomb2, L. and Alaba2, T.E., et al.The Effects Of Steamed Broccoli Sprout Consumption On Gut Microbiota In Healthy Adults And Adults With Self-Reported Bowel Conditions  In preparation.
  15. Beijbom, O’Doherty, Beiko, Ishaq, Allen-Vercoe, Choudoir, Silva. 2025. Microbiome Stewardship (MiSt): Definition and Guiding Principles for Implementation. In preparation. 
  16. Alaba2, T.E., Holman2, J.M., et al. Broccoli Sprouts Alleviate Ulcerative Colitis in Mice By Increasing Dietary And Microbial Metabolites: Differential Effects In Young And Adult Male And Female Mice. In preparation. 

Presentations

I had a very active year for presentations, and I was able to participate because of the funding support provided from the institutions that graciously invited me (some of which I forgot to take photos of). I also traveled to D.C. twice for ASM Board meetings this year, and Guelph, Ontario for a research collaboration meeting. Sadly, due to the reductions and delays in federal funding in 2025, my lab could not afford to travel to conferences.

  1. “Place and Time Matter for Gut Microbes Making Anti-Inflammatories from Broccoli Sprouts”, Microbiology and Molecular Genetics departmental seminar series at the University of Vermont, Burlington VT, Oct 24, 2025.
  2. “Place and Time Matter for Gut Microbes Making Anti-Inflammatories from Broccoli Sprouts”, Distinguished Lectures in Microbiology at the University of Wisconsin, Madison, Oct 2, 2025.
  3. Ishaq, S. Partnerships with gut microbes to improve health. South Dakota State University College of Pharmacy and Allied Health Professionals Convocation. Brookings, SD. April 23, 2025. (invited keynote)
  4. Richard*, H., Ishaq, S., et al. How microbial monitoring could bring new insights into salt marsh ecosystems impacted by tidal restrictions. Coastal and Estuarine Research Federation meeting. Norfolk, VA. Nov 9-13, 2025.
  5. Ishaq, S. Microbiome Stewardship…. What is that? Conservation in a Microbial World meeting to provide recommendations to the International Union for the Conservation of Nature (IUCN). La Jolla, CA. May 12-14, 2025. (invited)
  6. Holman2, J., Kirkendall2, A., Sharma1, A., Nowak1, L., Li, Y., Ishaq, S. Novel broccoli-sourced anti-inflammatory conversion in mouse-gut bacterial isolates. UMaine Student Research Symposium, Orono Maine, April 11, 2025.
  7. Kirkendall2, A., Holman2, J., Sharma1, A., Nowak1, L., Adjapong, G., Li, Y., Ishaq, S. Putative Anti-inflammatory Producing Gut Bacteria lessen IL-8 production in Cells from a Patient with Ulcerative Colitis.  UMaine Student Research Symposium, Orono Maine, April 11, 2025.
  8. Ishaq, S. Testing out an immunological mouse model of inflammation as a means of assessing diet to reduce symptoms. University of Vermont 2025 Neuroscience, Behavior, and Health Forum. Burlington, VT. February 1, 2025.

And from teams I collaborate with:

  1. Miles*, M., Kantar, L., Simpson, B., Ishaq, S.L., De Urioste-Stone, S., Kamath, P. Characterization of Microbial Communities in Winter Ticks & Moose in Maine​. European Society for Evolutionary Biology (ESEB) 2025 Congress. Barcelona, Spain. August 17-22, 2025.
  2. O’Doherty*, K.C., Allen-Vercoe, E., Beiko, R.G., Choudoir, M.J., Ishaq, S.L., Silva, D. Microbiomes and critical health psychology: Social equity, culture, and environments. International Society for Critical Health Psychology. Galway, Ireland. July 1-4, 2025.
  3. Escudero Alejos*2, B., J. B. Poblete,M. Chusho Guevara, A. P. Jimenez Lagos, J. M. Sandro, A. S. Mindiola, S. L. Annis, G. Pereira, L. Ferraretto, E. Cole Diepersloot, J. P. Alvez, Y. Jiang, M. A. Quaassdorff, T. Stahl, S. Ishaq, L. Stevens-Rosa, E. Herrero, H. R. L. Neto, E. Rodberg, and J.J. Romero.  Fungal, nutritional, and mycotoxin composition of alfalfa-grass hay mixtures samples from the northeast and northcentral regions of the United States. American Dairy Science Association. Louisville, KY. June 22–25, 2025.
  4. Beiko*, R., Choudoir, M.J., Ishaq, S.L., Silva, D.S., Allen-Vercoe, E., O’Doherty, K.C. Microbiome Stewardship Is Necessary, But What Exactly Should We Steward? Canadian Society of Microbiologists 7th Annual Conference. Université de Montréal, Quebec. June 17-20, 2025.

I also gave an interview on a podcast/webinar this year:

  1. “The gut healing power of microbes and cruciferous vegetables.”, Meet the Microbiologist Podcast, Interviewed by Ashley Hagen, Aug 28, 2025. 

Research

Broccoli sprouts once again dominated our research agenda with a handful of ongoing projects. Most of those are still in progress, so we don’t have detailed information to share yet, but here are some summaries.

96 well plate
Spectrophotometer

We spent much of the year in the lab working on a 24-hour plate-based assay to screen >330 bacteria for growth in the presence of glucoraphanin under different conditions. This required the help of many of the graduates and undergraduates, and me! We identified 32 bacteria that were of interest to us because they grew better or worse in the presence of glucoraphanin in their culture media as compared to just being in just the culture media alone. We using Sanger Sequencing of the 16S rRNA gene to get a quick identification of our bacteria, then proceeded with whole-genome sequencing to get a high-resolution identification of the bacteria, as well as which genes they posses.

We conducted RNA transcriptomics on a few bacteria to see which genes were up/down regulated (used more or less) when they were grown with glucoraphanin versus without it. Since very little previous research has been able to identify the genes that bacteria use to convert inactive glucosinolates into anti-inflammatory and anti-oxidant isothiocyanates, we are hoping the genomic and transcriptomic data gives us a list of possible genes to target for future research. Now that we have identified which bacteria can convert glucoraphanin into sulforaphane, we can test them out as possible probiotics to resolve Inflammatory Bowel Disease. Our work this year has been graciously supported by the UMaine Institute of Medicine, and student research awards from the Biomedical Association of Maine.

Here I am making up a plate for the bacterial culturing trial.

I have also been busy with conceptual research (not lab-based) this year. Along with three different research groups, I have been writing manuscripts, giving presentations, and designing workshops broadly around improving the process of science.

Much of that has been related to the Microbiome Stewardship working group, funded by the Canadian Institute for Health Research, and featuring Drs. Kieran O’Doherty, Rob Beiko, Emma Allen-Vercoe, Mallory Choudoir, and Diego Silva, as well as Lola Holcomb. Over several years, out working group will generate a working definition and framework for the concept of microbiome stewardship, which is essentially that we should use policy and practice to ensure we don’t degrade the microbial ecosystems which are critical to life on earth. We will also foster case studies on how other researchers have integrated their microbiome science with equity, education, or policy to make a bigger impact. We published a prospective piece, and hope to publish our working definition in 2026.

In July 2025, the Stewardship group, along with the Microbes and Social Equity working group, hosted a research summit on microbiome stewardship, which was held virtually when federal funding was cut off in early 2025 for conferences. The summit was a success, and really elevated our conversations on the practicality of microbiome stewardship, which culminated in a research group workshop in Dec 2025.

Microbes and Social Equity working group

The MSE group has more than 350 members, and about 150 additional people just subscribed to our newsletter. Last year, we added an elected Board of Directors, who spent much of the year drafting By-Laws for group governance, a Code of Conduct, and the beginnings of a Strategic Plan. In 2026, the MSE Board votes to enact these.

We migrated the MSE webpage over to its beautiful new site, hosted and maintained by Applied Microbiology International. MSE was awarded the 2025 Dorothy Jones Diversity and Inclusion Achievement Award.

In 2025, we stuck with the monthly seminar series, and began to partner with Applied Microbiology International to help us promote events. These events attracted >380 attendees or viewers of the recordings and >900 registrations, and while these numbers are slightly lower than previous years, we attribute this to the reduced number of events (9 instead of 12, as the speakers in February, August, and December needed to reschedule in 2026 due to personal constraints). Some of the seminar recordings can be viewed here.

Speaker nameInstitutionTitle of the Talk
Adina Howe, PhDIowa State Univ.The Scoop on Poop:  Agricultural microbiomes and social equity
Adriana Romero Olivares, PhDNew Mexico State Univ.Fungal responses to global climate change and potential impacts to our ecosystems and public health
Geo Santiago-Martínez, PhDUniv. of ConnecticutThe role of methane-producing anaerobes in One Health
Julianne Meisner, BVM&S, MS, PhDUniv. of WashingtonRelational One Health: a more-than-biomedical approach to more-than-human health
Chelsey Spriggs, PhDUniversity of Michigan Medical SchoolViral Entry: Lessons from Pathogens to Improve Human Health
Landon Getz, PhDUniv. of TorontoDefending against Phage Predators: Trading Public Goods via Integrons
Kristen DeAngelis, PhDUniv. of Massachusetts AmherstHealthy Soils: Our Hope for a Warming World
Kat Milligan-McLellan, PhDUniv. of ConnecticutThe journey of one Inupiat through academia: Diversity Matters
Mathieu Groussin, PhDKiel Univ.Industrialization drives convergent microbial and physiological shifts in the human metaorganism

Teaching

This was a unique year for teaching, as I taught 2 AVS Capstone courses in the spring, but because I was on sabbatical (break from teaching and advising) in the fall, my 2 fall courses were taught by other instructors. But, it was still busy because I was overhauling one of those courses during the semester. I’ll tell you all about it in a post next 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.

Social Media

I expanded the social media reach of the lab by joining two new platforms in 2024, The Nova Integration Hub as I have been a member of the Nova Network for the past two years, and Bluesky. This expanded the number of followers >5,250 across those platforms and twitter, facebook, instagram, linked in, mastodon, and subscribers to my blog. The website attracted ~8,500 visitors and ~13,800 views, bringing it to >73,000 total visitors and >132,000 total views since 2016.

In 2025, I wrote >20,800 words across 50 blog posts, although many of these were event posts for the Microbes and Social Equity speaker series. My most popular post of the year is still the one on academic tenure with >8,400 views.

Looking ahead to 2026

The lab already has a lot planned for 2026! Johanna intends to defend her PhD dissertation in early 2026 and graduate in May, Heather will be defending hers and graduating in summer 2026. Ashley will take her comprehensive exam. Undergraduates Mia Poirier, Alexandra Ruff, and Aaron Williams will all be graduating in May and going on to bigger and brighter opportunities. We expect a bunch of new manuscripts on our current research to be submitted for peer review to scientific journals, and already have presentations planned at the UMaine Student Research Symposium. I’ll be in D.C. for Board meetings in March and June (as part of the ASM Microbe 2026 meeting), and I’m currently setting up guest lectures and seminars for next year (announcements forthcoming).

Other than all that, I’m looking forward to continuing the work-life balance I fought tooth-and-nail for all of 2025, and to continue to carve out time to paint. 2025 was an incredibly productive creative year for me, and something that helps me unwind and think about my work abstractly — the key to scientific discovery.

Happy New Year!

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