Author: sueishaqlab

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.

Working full time on your break from work: University Sabbaticals

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My sabbatical – a semester-long release from my teaching, undergraduate advising, and departmental administration duties – wrapped up at the end of December. Despite only having to ostensibly perform half my job, I worked full-time my entire sabbatical just to keep on top of my current workload because university ‘responsibility creep’ is too pervasive. However, being on sabbatical allowed me just enough free time during the work week to reflect in a way that I have not been able to afford in a long time – something avid readers of my blog might have noticed as my introspective content has been sparse and the length of my posts has diminished over the last few years. Case in point: I started the outline for this blog post in November 2024 with the intention of posting in January 2025todiscussmy sabbatical plans for fall 2025, and I am just now getting around to writing the summary of events at the end of January 2026.

What is a sabbatical and who takes over my responsibilities?

A sabbatical is broadly used to describe a long break from one’s job responsibilities, but it is structured very differently based on career and institution. While it can mean an extended vacation bestowed on long-term employees after years of service, university sabbatical provides a temporary release from some responsibilities to allow faculty to improve other parts of their role/responsibilities. For example, many faculty use their sabbatical to visit another lab to launch a collaborative project or learn a new technique, others use it to learn new topics to expand their teaching repertoire. Institutions may set requirements for research or teaching objectives, but at UMaine the faculty propose their own goals in a written application. Faculty are eligible to apply for one or two semesters off every six years of service, and proposals are reviewed by the Department Chair, Dean’s Office, and Provost’s office before some are approved.

For example, UMaine’s guidelines and application for sabbaticals is here. You’ll note that only a certain number of sabbaticals may be approved for each campus in the UMaine system each year, regardless of how many people are eligible. Thus, the application materials (your proposal) are import because, from the UMaine guidelines, “The selection of those who will receive these sabbaticals shall be based on a program proposal which includes a statement of intent and on benefits of the proposed sabbatical to the individual, the campus and the profession.”

Asking for one semester off (4 months) versus two (the 9-month academic year) creates different challenges for one’s department, as my duties don’t vanish when I’m not there. Sabbatical proposals require faculty to describe how our existing responsibilities will be met. My undergraduate advisees needed to be reassigned to my colleagues in the Animal and Veterinary Science program (some of whom had to resolve enrollment and academic admin barriers for 50 undergraduates), I needed to find adjuncts with highly-specialized academic backgrounds to teach my two fall courses (totaling 130 students), and critical decisions still needed to be made to help the program and department survive the university-wide restructuring and budget cuts that stemmed from the year of chaos in federal funding for research and education.

Luckily, my department had room in the budget to hire two adjuncts, because when faculty take one semester of sabbatical off, we still draw 100% of our salary (half of mine is for research, half is for teaching/advising, and we are required to provide departmental administration and university service for free). Thus, I needed to have my sabbatical plan approved in advance by my departmental chair to ensure we had money to hire temporary replacements. If I had taken a year off, my salary would have been reduced by 50% for that year, and the remainer would have been used to pay for a temporary employee to teach/advice 12 credit hours over 9 months.

Of course, some responsibilities cannot be re-assigned or paused, so I was still obligated to perform some teaching, advising, and admin duties even though I was ostensibly freed from those. I reflect on that towards the end of my post, after I talk about my goals.

Sabbatical Goal 1: Flipping AVS 254 Intro to Animal Microbiomes

My primary goal was to transform my existing lecture-based course, AVS 254 Intro to Animal Microbiomes, into a flipped-classroom format in which all lectures are recorded ahead of time for students to watch at their convenience, and the scheduled class time is spent on active learning and completing assignments. I completed this objective, but it took me 7 months instead of 3 because of the extensive burden of generating curriculum (literature review, summarizing info, finding or creating images and diagrams, making content visually accessible, writing presenter notes for all slides, finding journal articles which were easy to read for homework, designing walk-through assignments which teach research skills). Flipping the classroom can benefit the students, by providing more opportunities to connect learning material with skills and problem-solving. I also needed much more time than expected to complete my objectives because of the teaching and advising which couldn’t pause during my sabbatical.

Flipping the classroom made better use of my time and expertise by allowing problem-solving assignments. While it takes extensive expertise to complete the literature reviews and summaries for my lectures (which are each on a different topic), reciting the content of my lectures each year is not a good use of my time. Instead, recording my lectures allows me to use classroom time to provide my expertise to students on assessing and using information on microbes to solve problems. In previous years, I flipped several lectures and use class time for active learning, which was very successful. For my sabbatical, I revised all the course assignments from at-home writing to in-person research-based activities: how to use databases to analyze microbiome data and compare DNA sequences, compare existing data on microbiomes and interventions, choose one technology versus another, design hypothetical experiments or interventions, and generate action plans for hypothetical collaborations. The flipped classroom creates asynchronous learning of course material, which is also part of a long-term revision to the modalities of my course that I’ve been working towards for several years. Last year, and starting again next year, I will offer my course with an in-person version (the flipped classroom), and as an asynchronous version.

Recording content allowed me to improve depth of material. To condense the material from three lectures per week into two per week (or one/holiday week), I restructured my 35 lectures into 28. This involved moving content rather than cutting it, and allowed me to condense similar material into one lecture instead of dispersing it to work within the time limit of in-person courses. By recording lectures, I was able to double the amount of content provided and go into more depth without increasing total lecture time, because the recordings proceed faster than live lectures.  For example, in a lecture on how diet affects microbial communities in monogastric animals, I was able to add comparative anatomy, physiology, microbiology as well as integrate more biophysics of digestion, and collectively this allowed me to tie science from multiple disciplines into a cohesive narrative about how host species and diet both affect gut microbes.

Recording content allowed me to make materials more accessible. First, no matter how I structure my content, some students feel like there is too much material while others feel there is not enough. To provide a “Goldilocks Zone”, the recordings can be played at low or high speed to keep pace with their learning style. Second, no matter how many students indicate they want in-person courses, only about 1/3 are able to show up the entire semester, and that falls to 1/10 every time (according to students) a science “weeder course” has an exam as students are given little-to-no flexibility on deadlines for those courses and are forced to de-prioritize (and risk failing) another course. I’ve spoken to students who have said they chose to skip assignments or accept a worse grade in my course instead of falling behind in chemistry because they knew I would let them turn in assignments weeks or even months late while they receive little flexibility for life events which prevent them from attending class/lab or completing assignments on time. To combat this, all my recorded lecture content is available at the beginning of the semester for students who need to complete this course at custom intervals instead of weekly.  The asynchronous version accommodates students who have too many courses, work, long commutes, medical constraints, family care duties, or other obligations which preclude them attending and engaging with the course. This, too, presented a challenge as I needed to create protocols or walkthroughs which can be accomplished within the classroom as well as online, and make them expandable to create extra objectives for students completing assignments in a group to maintain equitable workloads with online students completing assignments solo.  

 Recording the lectures required an overhaul of all materials to make them higher quality, self-explanatory, and to make them more inclusive to learning assistance technology. In addition to generating more content, all slides needed to be recorded which required presenter notes/ a script to improve the quality of the recording and reduce the use of filler words. To improve content for non-visual learners (visual disability or those who listen to the audio recording at work without looking at the slides, this also required a significant time investment to describe each graph, diagram, or other visual element in my presenter notes/audio recording. By adding presenter notes on slides, I could also create annotated PDFs versions of lectures that are easier for students to use with screen-readers, and easier to download for students with low-quality internet, and allows students to have a written script for the video version as the subtitle-generating AI in Kaltura sometimes struggles to accurately transcribe scientific terms or certain words because of the way I speak.

Students were enthusiastic about the updates to the course content and format, based on course evaluations from Fall 2025 when an adjunct taught my course but I was making course revisions in advance of releasing course material each week. Student comments included:

  • “I loved that this course was offered online. As a dual–enrolled student, this made it possible for me to take the course. I also really appreciated the flexibility of deadlines. I feel that it was very reasonable to simply ask for more writing if the assignment was late. Thank you!”
  • “I appreciate how the lecture slides are in video and pdf format. This allowed me to watch the lecture and then follow up on parts I may have missed with the pdf.”
  • “I found the assignment that we did each week on the focused topic the most valuable in the course. I always found myself going way overboard on the assignments because I enjoyed learning about the topics/questions that I was investigating. I also liked how the assignments gave us some freedom as it allowed us to choose whatever animal species to research and not too constricting which made it more fun and engaging.”

Sabbatical Goal 2: Updating course materials for data analysis

The second goal for my sabbatical was to update the course materials for my data-analysis based AVS 454/554 DNA Sequencing Data Analysis Lab. Unfortunately, I did not even get to begin this objective because of the extensive effort to revise AVS 254 and my persistent workload was too high. However, I did receive useful feedback from the adjunct instructor who taught my course while I was on sabbatical. This data analysis lab uses coding in several programs to analyze DNA sequencing data and generate draft manuscripts. Updating the materials would benefit me by making this course cutting-edge and streamlined, as these programs, and the theory behind the data analysis workflow, evolve on an annual basis in the rapidly changing field of microbial ecology. The feedback I received indicated that graduate students needed more remedial content, especially a basic understanding of statistics and a more thorough explanation of how to apply those statistics to their experiments and microbial community analysis.  As such, when I can update this course, I will expand my existing 4 lectures on statistics to 6.

Sabbatical Goal 3: Catching up on research

My third sabbatical goal was to catch up on my tasks for completed and in-progress research, as well as to add new components to my work, which I successfully completed. My research on how broccoli sprouts in the diet can induce gut microbes to reduce inflammation has been adding new facets over the past year which require more of my attention, including metagenomics, whole genome sequencing, transcriptomics, protein identification and enzyme isolation, and probiotic development.

My sabbatical allowed me the time to write/revise seven scientific manuscripts for peer review, provide three presentations of my work to research and student audiences, to help one of my graduate students write their PhD dissertation in preparation for their defense, to help one of my students prepare for and take their comprehensive, to provide graduate committee support for two students to defend and another to take their comprehensive exam, and to plan/perform an intensive probiotic trial in mice. In addition, I spent the fall revising three large-scale, multi-year, multi-institution funding proposals to USDA NIFA and NIH.

I was also able to complete more research administration and leadership opportunities, such as fostering research case studies through my role on the Microbiome Stewardship research group, leadership duties for the Microbes and Social Equity working group, an international research society, and participating in research-curation initiatives such as the creation of a Microbe Specialist group for the IUCN.

My teaching was reallocated during my sabbatical, but course revision was more intensive than previous years

I teach 2 courses each semester, three of which are required for AVS undergraduates, and one of which teaches a specialized data analysis to graduate students which need it to perform their research. Luckily, I was able to find local expertise for my two fall classes, which are highly specialized topics and difficult to find replacements for in Maine. My data analysis course was taught by a faculty member in the bioinformatics master’s program at UMaine, who has significant experience teaching coding for data sciences. My animal microbiomes course run by one of my PhD students, Ashley, who was a grader for the course last year and had gained familiarity with the content and delivery of the course. To help her manage the 97-undergrad course, it was held in an asynchronous format, in which all lectures were pre-recorded by me and students could access content and complete assignments at their convenience each week.

However, this year’s course was a challenge for both of us: I was actively revising the lectures, reading list, and assignments during the semester in an effort to keep pace with the overhaul objectives of my sabbatical. I had intended to revise at least half the source over the summer, when I was without summer salary and ostensibly should not have been working, but I had so many service (unpaid), research, and advising activities, as well as the course revision, that I worked full-time all summer. I was able to revise most of the first third of the course over the summer, which bought me time in September and October when I was still working full – or more than full—time despite being on sabbatical: the amount of service, advising, and research once again overwhelmed my schedule. In addition, I had to spend September and October revising two large-scale, multi-year, multi-institution funding proposals because of the deliberate delays to the USDA NIFA and NIH research funding mechanisms in 2025 delayed reviews on previously submitted proposals, and for the USDA funding, pushed proposal submission deadlines from the summer to the fall. Thus, by November I was rushing to revise course content to stay ahead of the syllabus.

Despite being off contract (unpaid) all summer, and despite being on sabbatical and freed from teaching and advising and admin all fall, I put in 40 hours a week on course revisions, evaluating graduate student performance in comprehensive exams and defenses, writing recommendation letters for undergraduates and graduates, oh, and teaching and assisting with departmental administration. That’s right, I taught 4 students during my sabbatical going through their Capstone courses out of sync to help them graduate. And, because of the university strategic revising evaluation (we got marked down for having too high of a student: faculty ratio even though the university has not given us permission to hire more faculty despite our increasing enrollment in the last 5 years) and subsequent requests to slash departmental budgets (without reducing our workload or number of students), I attended hours of administrative meetings and helped write a plan for our program in response to the SRE.

My advising was reallocated during my sabbatical, except for all the unpaid advising university faculty typically do

The sabbatical provided temporary relief to my heavy workload and a chance to catch up a little, but by no means did it resolve the burden of increased responsibilities, as enrollment or student needs increase but the number of faculty per student does not. In fact, being on sabbatical allowed me to work at a sustainable 40 hours per week instead of the 50+ hours per week I am pressured to work every semester through the number of student, colleague, and university requests for my help. Yet, during my sabbatical, I still had advising and teaching that could not be re-allocated, and departmental activities still needed effort, such as making decisions about spring courses or providing timely information to the university due to the strategic revisioning plan.  I bring this up as a way to demonstrate how valuable sabbaticals are and re-enforce the support for sabbaticals at the college level. I urge the university to find creative ways to allow faculty to extend their sabbaticals to one full academic year without having to take the full-year-sabbatical reduction in pay.

The changes to federal education and research funding, as well as the overall economy, changed academic timelines for many students. In 2025, I advised three graduate students, and was on the thesis committee for two more, who needed to graduate sooner than expected due to federal delays in graduate research fellowships which left them without salary. Similarly, my previous advisees needed letters of recommendation to apply for veterinary or medical programs, or jobs. I wrote 13 letters (totaling 13 hours) this summer (when I am off contract) and fall.  This fall, I had 4 students who needed to take the AVS Capstone courses to graduate on time, so I was still performing some teaching tasks (paid through add comp). This has become a regular occurrence as, based on student feedback, the reduction in faculty at UMaine has reduced available courses and made enrollment much more difficult – essentially, I am asked by students to teach my courses out of their designated semester because they need help to graduate early because they cannot afford another semester. Students need more flexibility in their course availability and they need help year-round, and providing summer salary or sabbaticals offers faculty a way to accommodate students while still accomplishing our other tasks.

My sabbatical was an incredible opportunity

For anyone who is considering a sabbatical, I absolutely recommend it. You don’t need to make grand plans, or do something completely novel, or even resolve your entire pile of unfinished business for your sabbatical to be successful. View it as a “stay-cation”, and a way to check the 1000 tiny items off your to-do list that couldn’t be accomplished because of the perpetually hectic pace of academia. If you think you are too busy to take a sabbatical, then you really need to. It may seem like I wasted my sabbatical on work or old, unfinished business, but it allowed me to free myself from lingering obligations, make improvements to teaching or advising to make my job run more smoothly, and importantly, it helped me gain back some time to think and write which are critical aspects of my job that continuously get de-prioritized by urgent requests for my time (meetings, emails, and having to drop everything and work on requests for information from the college). And, I had more time to paint in 2025 than I have had in years. I will have to wait 6 years to be eligible for my next sabbatical, but I’m already looking forward to it!

Ashley advances to PhD Candidate in the Human Nutrition and Food Sciences doctoral program!

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Human-nutrition-powerhouse Ashley Reynolds passed the graduate comprehensive exam today to advance to candidacy in her Human Nutrition and Food Science PhD Program at Umaine!! Now that she is a PhD Candidate, she is eligible to apply for federal funding for graduate fellowships, and she’ll be focusing on her dissertation research. She’s previously obtained a master’s of science and registered dietician status, and her extensive experience in nutrition and health is now being used to expand the scope of our broccoli sprout/gut microbes research to evaluate the effect on neuroinflammation. She has a literature review that will be sent out for peer review soon, and this year will complete a lot of lab work. Ashley learned how to handle mice on a recent project. Here she is weighing the first mouse she learned to pick up. She’ll be evaluating inflammation in the gut and brain using tissue samples for histology, and blood for immune factors.

Johanna, Ashley, Alexis, and Sue wearing gloves, hairnets, booties, and gowns, and standing in front of racks of mice.
Johanna, Ashley, Alexis, and Sue put in long hours during the mouse trial to collect samples each day.
Ashley is holding up a plastic jar with a research mouse in it.
Ashley learned how to handle mice on this project. Here she is weighing the first mouse she learned to pick up.

Headshot of Ashley Reynolds weiring a beige sweater.

Ashley Reynolds, M.S., R.D.

Doctor of Philosophy candidate, Human Nutrition and Food Sciences. Ashley is being co-advisor by Dr. Yanyan Li at SUNY Binghamton  

Ashley began her academic journey at the University of Maine completing her undergraduate degree in Food Science and Human Nutrition in 2021 as a Maine Top Scholar. Ashley then pursued a Master’s degree in Food Science and Human Nutrition at the University of Maine. Ashley’s master’s degree research focused on exploring intuitive eating in college students. This research aimed to understand and promote a healthy relationship with food among this demographic. She also took on the role of a teaching assistant for several nutrition classes while completing that degree. In 2023, Ashley successfully completed a dietetic internship and shortly after passed her RD exam to become a registered dietitian. Currently, Ashley is back at the University of Maine, pursuing her Ph.D. in Food Science and Human Nutrition. She is incredibly interested in nutrition therapy and is beginning her research looking into the microbiome and metabolomic pathways in the context of IBD. The current research uses both human and mouse data to determine the effects broccoli sprouts has in individuals with IBD.

MSE virtual seminar today: “Mystery at the Membrane: Discovering Copper’s Entry Route into Bacteria and Other Copper Tales”

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The MSE logo is a scale for comparing weights of two things, with microbes being weighed on both sides.

Events will be hosted January – December in 2026, on the last Wednesday of every month, 11:00 – 13:00 pm ET. Presented over Zoom.

After each talk, we will continue the discussions in an informal social meeting with MSE. All speakers and members of the audience are welcome to join the social meeting.

Hosted by: Sue Ishaq, MSE, and finacially supported by the University of Maine Institute of Medicine, and the Applied Microbiology International via the 2025 Dororthy Jones Diversity and Inclusion Acheivement Award.

Registration is required but free. Click here to register!

Registration to the seminar and social hour is free, but required. New this year: the live session will be available free, but the on-demand video-recording will only be available to MSE members for the first year (and available to the public afterwards).

Summary: 

Microorganisms are critical to many aspects of biological life, including human health.  The human body is a veritable universe for microorganisms: some pass through but once, some are frequent tourists, and some spend their entire existence in the confines of our body tissues.  The collective microbial community, our microbiome, can be impacted by the details of our lifestyle, including diet, hygiene, health status, and more, but many are driven by social, economic we, medical, or political constraints that restrict available choices that may impact our health.   Access to resources is the basis for creating and resolving social equity—access to healthcare, healthy foods, a suitable living environment, and to beneficial microorganisms, but also access to personal and occupational protection to avoid exposure to infectious disease. This speaker series explores the way that microbes connect public policy, social disparities, and human health, as well as the ongoing research, education, policy, and innovation in this field. 

You can find recordings from previous series here.

“Mystery at the Membrane: Discovering Copper’s Entry Route into Bacteria and Other Copper Tales”

Dr. Michael Johnson, PhD

Jan 28, 2026, 11:00 – 13:00 ET.

Dr. Michael D. L. Johnson received an A.B. in Music from Duke University and his Ph.D. in Biochemistry and Biophysics at the University of North Carolina at Chapel Hill. He completed two postdoctoral fellowships in Infectious Diseases and Immunology at St. Jude Children’s Research Hospital. Currently, Dr. Johnson is an Associate Professor at the University of Arizona in the Department of Immunobiology, where he studies mechanisms of metal toxicity in bacteria. He was the 2020 NIGMS Director’s Early Career Investigator Lecturer and the 2022 American Society for Microbiology William A. Hinton Award winner for Advancement of a Diverse Community of Microbiologists. Dr. Johnson is active in trainee professional development through developing the National Summer Undergraduate Research Project, The BIO5 Postdoctoral Fellowship Program, and as the Associate Dean for Basic Science Research and Graduate Studies for the College of Medicine Tucson. His faculty page is here.

Dr. Johanna Holman successfully defends her doctoral dissertation!

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Congratulations to the newly minted Dr. Johanna Holman for successfully defending her doctoral dissertation in Microbiology today! The Ishaq Lab will be celebrating together in-person in a few weeks, when we’re all past cold season. In the meantime, Johanna will put the final touches on her thesis, and start converting those chapters into manuscripts for journal publications! She’s also preparing to transition to a postdoctoral research position (details to follow).

The recorded presentation of her work is here, and focuses on her work exploring which gut bacteria metabolize glucosinolates in broccoli sprouts and produce the anti-oxidant sulforaphane, as well as how the do it, and whether they will do it in different circumstances.

Johanna joined my lab in 2020, first as a master’s student in Nutrition, then as a PhD student in Microbiology. She started her research career as a lab tech for some of my long-term collaborators, Yanyan Li and Tao Zhang, back when they were at Husson University in Bangor, Maine. She joined my lab to add microbiology to her existing nutrition and biochemistry background, and at this point, it might be easier to list which projects she hasn’t been a part of. She’s performed bacterial culturing, bacterial community analysis, genomics, transcriptomics, and protein prediction. She’s run diet intervention trials in mice and in people, and she’s trained nearly every student in my lab in the last 6 years in some type of lab work or data analysis. She has been a valuable collaborator on our intricate and lab-heavy projects, allowing the lab to coordinate up to 5 projects and 8 students simultaneously.

Johanna is a brilliant nutritional health microbiologist who uses multi-faceted research – from the lab to public health – to understand the connection between health and the microbiome. She’s led two publications from her masters (a literature review on sulforphane and the immune system, and another on a broccoli sprout diet intervention in mice); co-authored three others (a literature review on cruciferous vegetables, a similar broccoli sprout diet intervention in mice, and a different formulation of the broccoli diet); and has several more manuscripts from her doctoral work that are poised for submission to scientific journals for peer review.

She’s written graduate research proposals for the NIH and USDA. She was awarded the Charles Morris and UMaine grad student award.

She’s been a teaching assistant for chemistry and biology, with an estimated 120 students per year. She’s a graphic designer (Imaginome Designs). She grew a whole human from scratch. She’s keen to learn and has always kept an open mind to new opportunities. Johanna has been instrumental in the knowledge generation and success of my lab, and we are so luck to have been a part of her journey.

A cartoon of a woman eating broccoli, with the digestive tract shown on her shirt, and smiling microbes in the background.
A diagram with two panels, and a cartoon mouse in the middle. The cartoon mouse is eating broccoli, and a cartoon of the digestive tract is overlaid on the mouse's abdomen. Lines emanating from the broccoli point to the left panel, and show the compound glucoraphanin being converted into sulforaphane by the myrosinase enzyme. Lines emanating from the colon of the mouse point to the panel on the right, showing the same biochemical conversion by gut microbes.
A black and white portrait of Johanna Holman
A logo that says "The Broccoli Project"
A cartoon of brightly colored, smiling bacteria.
A cartoon of cruciferous vegetables
Johanna Holman standing at a wooden podium with a white board and a projection screen behind her. Johanna is presenting her master's thesis, and the title slide of the presentation is showing on the screen.
Person in a research facility holding up their arm with a mouse on it. Person is wearing a hairnet, nitrile gloves, surgical mask, and a surgical gown. They are holding their left arm up to the camera to show off a mouse with dark brown fur sitting on their arm. In the background is a metal shelf with containers of research materials.

MSE virtual seminar Jan 28: “Mystery at the Membrane: Discovering Copper’s Entry Route into Bacteria and Other Copper Tales”

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The MSE logo is a scale for comparing weights of two things, with microbes being weighed on both sides.

Events will be hosted January – December in 2026, on the last Wednesday of every month, 11:00 – 13:00 pm ET. Presented over Zoom.

After each talk, we will continue the discussions in an informal social meeting with MSE. All speakers and members of the audience are welcome to join the social meeting.

Hosted by: Sue Ishaq, MSE, and finacially supported by the University of Maine Institute of Medicine and Applied Microbiology International.

Registration is required but free. Click here to register!

Registration to the seminar and social hour is free, but required. New this year: the live session will be available free, but the on-demand video-recording will only be available to MSE members for the first year (and available to the public afterwards).

Summary: 

Microorganisms are critical to many aspects of biological life, including human health.  The human body is a veritable universe for microorganisms: some pass through but once, some are frequent tourists, and some spend their entire existence in the confines of our body tissues.  The collective microbial community, our microbiome, can be impacted by the details of our lifestyle, including diet, hygiene, health status, and more, but many are driven by social, economic we, medical, or political constraints that restrict available choices that may impact our health.   Access to resources is the basis for creating and resolving social equity—access to healthcare, healthy foods, a suitable living environment, and to beneficial microorganisms, but also access to personal and occupational protection to avoid exposure to infectious disease. This speaker series explores the way that microbes connect public policy, social disparities, and human health, as well as the ongoing research, education, policy, and innovation in this field. 

You can find recordings from previous series here.

“Mystery at the Membrane: Discovering Copper’s Entry Route into Bacteria and Other Copper Tales”

Dr. Michael Johnson, PhD

Jan 28, 2026, 11:00 – 13:00 ET.

Dr. Michael D. L. Johnson received an A.B. in Music from Duke University and his Ph.D. in Biochemistry and Biophysics at the University of North Carolina at Chapel Hill. He completed two postdoctoral fellowships in Infectious Diseases and Immunology at St. Jude Children’s Research Hospital. Currently, Dr. Johnson is an Associate Professor at the University of Arizona in the Department of Immunobiology, where he studies mechanisms of metal toxicity in bacteria. He was the 2020 NIGMS Director’s Early Career Investigator Lecturer and the 2022 American Society for Microbiology William A. Hinton Award winner for Advancement of a Diverse Community of Microbiologists. Dr. Johnson is active in trainee professional development through developing the National Summer Undergraduate Research Project, The BIO5 Postdoctoral Fellowship Program, and as the Associate Dean for Basic Science Research and Graduate Studies for the College of Medicine Tucson. His faculty page is here.

Announcing the 2026 MSE Speaker Series!

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MSE is back with another stellar lineup for the virtual seminar series, which will be hosted monthly through 2026. After each seminar, we will host an informal virtual social hour, in which attendees can chat with the speaker and MSE members about research, teaching, our pets, and more. 

Registration to the seminar and social hour is free, but required. New this year: the live session will be available free, but the on-demand video-recording will only be available to MSE members for the first year (and available to the public afterwards).

The MSE logo is a scale for comparing weights of two things, with microbes being weighed on both sides.

Events will be hosted January – December in 2026, on the last Wednesday of every month, 11:00 – 13:00 pm ET. Presented over Zoom.

After each talk, we will continue the discussions in an informal social meeting with MSE. All speakers and members of the audience are welcome to join the social meeting.

Hosted by: Sue Ishaq, MSE, and finacially supported by the University of Maine Institute of Medicine, and the Applied Microbiology International via the 2025 Dororthy Jones Diversity and Inclusion Acheivement Award.

Registration is required but free. Click here to register.

Summary: 

Microorganisms are critical to many aspects of biological life, including human health.  The human body is a veritable universe for microorganisms: some pass through but once, some are frequent tourists, and some spend their entire existence in the confines of our body tissues.  The collective microbial community, our microbiome, can be impacted by the details of our lifestyle, including diet, hygiene, health status, and more, but many are driven by social, economic we, medical, or political constraints that restrict available choices that may impact our health.   Access to resources is the basis for creating and resolving social equity—access to healthcare, healthy foods, a suitable living environment, and to beneficial microorganisms, but also access to personal and occupational protection to avoid exposure to infectious disease. This speaker series explores the way that microbes connect public policy, social disparities, and human health, as well as the ongoing research, education, policy, and innovation in this field. 

You can find recordings from previous series here.

“Mystery at the Membrane: Discovering Copper’s Entry Route into Bacteria and Other Copper Tales”

Dr. Michael Johnson, PhD

Jan 28, 2026, 11:00 – 13:00 ET.

Dr. Michael D. L. Johnson received an A.B. in Music from Duke University and his Ph.D. in Biochemistry and Biophysics at the University of North Carolina at Chapel Hill. He completed two postdoctoral fellowships in Infectious Diseases and Immunology at St. Jude Children’s Research Hospital. Currently, Dr. Johnson is an Associate Professor at the University of Arizona in the Department of Immunobiology, where he studies mechanisms of metal toxicity in bacteria. He was the 2020 NIGMS Director’s Early Career Investigator Lecturer and the 2022 American Society for Microbiology William A. Hinton Award winner for Advancement of a Diverse Community of Microbiologists. Dr. Johnson is active in trainee professional development through developing the National Summer Undergraduate Research Project, The BIO5 Postdoctoral Fellowship Program, and as the Associate Dean for Basic Science Research and Graduate Studies for the College of Medicine Tucson. His faculty page is here.

“Mechanisms of environmental microbiome resilience”

Feb 25, 2026, 11:00 – 13:00 ET.

Dr. Ashley Shade, PhD. is a Director of Research with the French National Center for Scientific Research at the University of Lyon, France. She studies microbial community ecology, biodiversity, and microbial responses to disturbances such as climate change. In 2024, she received the U.S. Presidential Early Career Award for Scientists and Engineers from President Biden for her work on microbial community resilience. As of 2025, she is the Editor in Chief of the scientific journal mSystems.

“Unravelling Periprosthetic Joint Infection”

Dr. Robin Patel, M.D.

Mar 25, 2026, 11:00 – 13:00 EDT.

Dr. Robin Patel is the Elizabeth P. and Robert E. Allen Professor of Individualized Medicine, Director of the Infectious Diseases Research Laboratory, Co-Director of the Clinical Bacteriology Laboratory, Vice Chair of Education in the Department of Laboratory Medicine and Pathology, and former Chair of the Division of Clinical Microbiology, at the Mayo Clinic. Professor Patel’s research focuses on understanding the inherent biology of periprosthetic infection. She has over 635 peer-reviewed publications, is supported by the National Institutes of Health and the Centers for Disease Control and Prevention, is the Director of the Laboratory Center of the Antibacterial Resistance Leadership Group of the National Institutes of Health, and is a Past President of the American Society for Microbiology where she currently serves in the role of Secretary on the Board of Directors. Her faculty page is here.

“Microbial Communities in the Leaves Around Us”

Dr. Naupaka Zimmerman, Ph.D. (he/him/his)

Apr 29, 2026, 11:00 – 13:00 EDT.

Dr Naupaka Zimmerman is an Assistant Professor in the Environmental Studies Program at the University of Kansas (KU). He was previously an Associate Professor of Biology and Director of the MS Biology Program at the University of San Francisco. His research explores microbial ecology, with a focus on the communities of fungi that live inside plant leaves without causing disease, known as endophytes. His work investigates how environmental conditions, host species, and geography influence the diversity and function of these microbes.

Born and raised on the Big Island of Hawaiʻi, Dr Zimmerman has studied the microbial ecology of native Hawaiian plants, particularly Metrosideros polymorpha. At USF, his lab worked on plant–microbe interactions in urban environments and sustainable agricultural systems, including research across San Francisco and at Star Route Farms in Marin County. He plans to extend that work to agricultural and grassland systems in the midwest in his new role at KU. His team uses fieldwork, microscopy, DNA sequencing, and bioinformatics to understand how plant-associated microbes contribute to ecosystem processes such as decomposition, plant health, and resilience to pathogens. His lab website is here.

“The nexus of food systems, ecosystems and human health: considering the more-than-humans who co-produce health”

Dr. Sarah Elton, PhD

May 27, 2026, 11:00 – 13:00 EDT.

Sarah Elton, PhD

Dr. Sarah Elton is an Assistant Professor and Eakin Chair in Critical Qualitative Health Research Methodology at the University of Toronto’s Dalla Lana School of Public Health. She researches at the nexus of food systems, ecosystems and human health, considering the more-than-humans who co-produce health, including microbes. In 2021, she was the first qualitative researcher to be recognized by the Gairdner Foundation when she won a Gairdner Early Career Investigator Award. Previous to her academic career, Sarah worked as a journalist and is the author of two Canadian bestselling nonfiction books, Locavore and Consumed: Food for a Finite Planet. In this presentation, she draws on more-than-human methodologies and her own field work in food systems to explore different ways social scientists can conduct research with microbes. She focuses on how critical qualitative research methodologies can enable scholars to investigate the social and political forces that shape human-microbe relations.

“TBD”

Jun 24, 2026, 11:00 – 13:00 EDT.

“The nuts and bolts of microbiome stewardship: what are we trying to protect?”

Dr. Rob Beiko, PhD

Jul 29, 2026, 11:00 – 13:00 EDT.

Dr. Robert Beiko is a Professor in the Faculty of Computer Science at Dalhousie University who specializes in the analysis of DNA and protein sequences to better understand biodiversity, evolution, and ecology. He is also Director of Data at Dartmouth Ocean Technologies, Inc. His lab is currently developing software tools and algorithms to better understand the evolution and transmission of antimicrobial-resistance genes, and new computational methods to identify species and infer their ecological roles using environmental DNA. His lab website is here.

“The Secret World Within: How the Microbiome Provides Insight into Gynecologic Health”

Dr. Nicole Jimenez, PhD

Aug 26, 2026, 11:00 – 13:00 EDT.

Nicole Jimenez, PhD

Dr. Nicole Jimenez is a postdoctoral fellow at the University of Arizona College of Medicine-Phoenix, specializing in gynecologic health research. Raised in Arizona, she was inspired by mentors in programs such as the Si Se Puede Foundation and ASU’s Los Diablos, and by her innate curiosity, to pursue a career as a scientist. She completed her doctoral degree in 2021 from Virginia Commonwealth University as part of the Vaginal Microbiome Consortium, studying the microbiome in the context of bacterial vaginosis, trichomoniasis, and pregnancy. Currently, her postdoctoral research, conducted in Dr. Melissa Herbst-Kralovetz’s lab, focuses on conditions such as chronic pelvic pain, endometriosis, adenomyosis, cervical and endometrial cancer, utilizing multi-omic pipelines, microbial culturomics, and 3D epithelial cell models. Dr. Jimenez has demonstrated a strong commitment to academic excellence, evidenced by recently securing the American Cancer Society postdoctoral fellowship, publishing manuscripts in microbiology and clinically focused journals, and receiving the 2025 University of Arizona Outstanding Postdoctoral Scholar Award. Driven by her passions for science, advocacy, and mentorship—having guided 22 students across various levels—she is actively preparing for a transition to an independent faculty position to continue her translational work on understudied gynecologic conditions through the lens of the microbiome. A recent article can be found here.

“Searching for missing gut microbes in the Amazon”

Dr. Emma Allen-Vercoe, PhD

Sept 30, 2026, 11:00 – 13:00 EDT.

Dr. Emma Allen-Vercoe obtained her BSc (Hons) in Biochemistry from the University of London, and her PhD in Molecular Microbiology through an industrial partnership with Public Health England. Emma started her faculty career at the University of Calgary in 2005, with a Fellow-to-Faculty transition award through CAG/AstraZeneca and CIHR, to study the normal microbes of the human gut. In particular, she was among the few that focused on trying to culture these ‘unculturable’ microbes in order to better understand their biology. To do this, she developed a model gut system to emulate the conditions of human and other animal guts and allow communities of microbes to grow together, as they do naturally.

Emma moved her lab to the University of Guelph in late 2007, and has been a recipient of several awards (through the Canada Foundation for Innovation) that have allowed her to develop her specialist anaerobic fermentation laboratory further. Emma is a Tier 1 Canada Research Chair, and her lab studies many microbial ecosystems, including those of Indigenous people of the Amazon, people in the industrialized world suffering from chronic disease, and those of honey bees and native pollinator insect species of Canada. Her faculty page is here.

“TBD”

Dr. Zinzi Bailey, PhD

Oct 28, 2026, 11:00 – 13:00 EDT.

“TBD”

Dr. Louis-Patrick Haraoui, PhD

Nov 25, 2026, 11:00 – 13:00 ET.

“Microbiome and Amazonian Indigenous Peoples, ethics and beyond”

Dr. Eglee Zent, PhD., and featuring Dr. Melissa Melby, PhD.

Dec 16, 2026, 11:00 – 13:00 ET.

Eglee Zent is the mother of two sons and has an eclectic academic background (art history, anthropology, botany, conservation biology). She conducted graduate studies at universities in Venezuela (Instituto Venezolano de Investigaciones Científicas, IVIC) and the USA (Georgia and California at Berkeley). She has carried out ethno-ecological, eco-cosmological, ethnocartographic and microbiome research in the high Venezuelan Andes among Paramero people as well as in the lowland Amazon among the Jotï, an Amerindian group. Her research embraces trans-disciplinary epistemologies and approaches, drawing in material and ideological, quantitative and qualitative, aspects. Eglee is an Assistant Professor of Human Ecology at the University of Vermont and her presentation features Melissa Professor of Anthropology at the University of Delaware

Logo designed by Alex Guillen

Johanna Holman prepares to defend her doctoral dissertation!

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Johanna Holman is preparing to defend her doctoral dissertation in Microbiology on January 27th!

The presentation of her work is publically available from 10 – 11 am EST, and will take place on Zoom (register here).

Johanna joined my lab in 2020, first as a master’s student in Nutrition, then as a PhD student in Microbiology. She started her research career as a lab tech for some of my long-term collaborators, Yanyan Li and Tao Zhang, back when they were at Husson University in Bangor, Maine. She joined my lab to add microbiology to her existing nutrition and biochemistry background, and at this point, it might be easier to list which projects she hasn’t been a part of. She’s performed bacterial culturing, bacterial community analysis, genomics, transcriptomics, and protein prediction. She’s run diet intervention trials in mice and in people, and she’s trained nearly every student in my lab in the last 6 years in some type of lab work or data analysis. She has been a valuable collaborator on our intricate and lab-heavy projects, allowing the lab to coordinate up to 5 projects and 8 students simultaneously.

Johanna is a brilliant nutritional health microbiologist who uses multi-faceted research – from the lab to public health – to understand the connection between health and the microbiome. She’s led two publications from her masters (a literature review on sulforphane and the immune system, and another on a broccoli sprout diet intervention in mice); co-authored three others (a literature review on cruciferous vegetables, a similar broccoli sprout diet intervention in mice, and a different formulation of the broccoli diet); and has several more manuscripts from her doctoral work that are poised for submission to scientific journals for peer review.

She’s written graduate research proposals for the NIH and USDA. She was awarded the Charles Morris and UMaine grad student award.

She’s been a teaching assistant for chemistry and biology, with an estimated 120 students per year. She’s a graphic designer (Imaginome Designs). She grew a whole human from scratch. She’s keen to learn and has always kept an open mind to new opportunities. Johanna has been instrumental in the knowledge generation and success of my lab, and we are so luck to have been a part of her journey.

A cartoon of a woman eating broccoli, with the digestive tract shown on her shirt, and smiling microbes in the background.
A diagram with two panels, and a cartoon mouse in the middle. The cartoon mouse is eating broccoli, and a cartoon of the digestive tract is overlaid on the mouse's abdomen. Lines emanating from the broccoli point to the left panel, and show the compound glucoraphanin being converted into sulforaphane by the myrosinase enzyme. Lines emanating from the colon of the mouse point to the panel on the right, showing the same biochemical conversion by gut microbes.
A black and white portrait of Johanna Holman
A logo that says "The Broccoli Project"
A cartoon of brightly colored, smiling bacteria.
A cartoon of cruciferous vegetables
Johanna Holman standing at a wooden podium with a white board and a projection screen behind her. Johanna is presenting her master's thesis, and the title slide of the presentation is showing on the screen.
Person in a research facility holding up their arm with a mouse on it. Person is wearing a hairnet, nitrile gloves, surgical mask, and a surgical gown. They are holding their left arm up to the camera to show off a mouse with dark brown fur sitting on their arm. In the background is a metal shelf with containers of research materials.

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!

Congrats to UMaine Grad Students on their first union contract!!

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Congratulations to the University of Maine Graduate Student Union on their first contract with the university system!! After years of negotiations and patience, the graduate students won greater recognition of their critical role as university employees, with that gratitude expressed as a livable wage (stipends had not increased in the 7 years I have been at UMaine despite the pandemic and cost of living inflation), partial health insurance coverage (costs were creeping up to 20% of their annual salary), partial dental coverage (they had no dental before), and tuition remission for select majors (to facilitate some much needed workforce development in Maine).

Read the UMS post and contract details here

Ideation in Ontario

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Last week in Guelph, Ontario, Canada, I had the unique please of “nerding out” with long-time colleagues (who I was meeting in-person for the first time) about microbial ecology questions that we wanted to answer, the science fiction we were reading, which metal band to listen to for the winter holidays, how to perform large-scale research on a tight budget, and whether the next season of whatever show had piqued our interest would be any good. The nerds-in-question are the Microbiome Stewardship research group, led by the intrepid Kieran O’Doherty, that I’ve been a part of for the past few years (and longer, counting the time we’ve collaborated through the Microbes and Social Equity working group).

Group photo of Left to right; front: Zhongzhi (Michael) Sun, Emma Allen-Vercoe, Sue Ishaq; middle: Mikaela Beijbom, Mallory Choudoir, Sarah Elton, Kieran O'Doherty, Panuya Athithan; back: Grace Gabber, Andreas Heyland, Rob Beiko.
Left to right; front: Zhongzhi (Michael) Sun, Emma Allen-Vercoe, Sue Ishaq; middle: Mikaela Beijbom, Mallory Choudoir, Sarah Elton, Kieran O’Doherty, Panuya Athithan; back: Grace Gabber, Andreas Heyland, Rob Beiko.

Over two days, my microbiome stewardship colleagues and I (both original team and expansion pack researchers) shaped our concept of what it means to share microbes between individuals, communities, and ecosystems; what it would mean to consider microbes as a natural resources to which everyone had an innate right to; and how it would look for public and planetary health to reduce the harm of human industry and consumerism to live more sustainably and regain all the benefits that the microbial world can provide us. Our of this meeting, we imagined what the focus of our next year or two of research will look like, as individual researchers and as a group, as we embark on the next phase of our multi-year project: case studies of how microbiome stewardship could be tailored, implemented, and evaluated. These studies will be published as they are completed and pass peer review, in a scientific journal online (announcement forthcoming).

This research ideation meeting followed two years of conversation, presentations, a symposium (sessions can be viewed here), journal articles, and a whole lot of research-, personnel-, and travel-coordination on the part of our research wrangler, Mikaela Beijbom, who has been helping us to organize our words and activities for the past 8 months.

As this tumultuous and combative year comes to a close, and as I prepare to end the “break” which was my semester-long sabbatical and return to 50-hour work weeks, the precious opportunity to let our minds wander – through work, life, and play – was a brief return to the pure joy of scientific discovery which drew us all to our careers. This year, scientists have faced hurdle after hurdle placed by the very public research institutions which were created to help us seek knowledge on behalf of the public good. Funding cuts have reduced the scientific workforce; lost precious time, expertise, and data; and disrupted the innovation and ideation process which research forges. Yet, the time I spent with colleagues last week was a reminder that knowledge generation, public good, scientific inquiry, and collaboration are values which cannot be defunded, banned, or curtailed so easily. As for our group, we’ll keep meeting (virtually, at least) throughout 2026 and beyond, for the love of science.