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.
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.
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.
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.
The Ishaq Lab is testing out some probiotics in mice this spring, as we look towards the next phase of our broccoli sprouts and gut microbiome work: generating solutions. It has been five years since our last mouse experiments, in part, because we have been busy digging into samples, data, and ideas from those studies.
We gained valuable insight into which and how gut bacteria might metabolize the inactive glucosinolates from broccoli sprouts – glucoraphanin being the one we focus on – and produce byproducts like sulforaphane which our gut cells can use to reduce the chemical and physical damage caused by inflammation or oxidation.
This process is easy in the lab and tricky in the real world – not everyone has the bacteria in their gut which can do it, some have the bacteria but they are not active, and some have the bacteria but they are making a different version of the byproduct which we cannot use.
For the past three years, we have been screening >300 gut bacteria to identify and select ones with the ability to grow in the presence of GLR and metabolize it into the byproducts SFN or SFN-nitrile (which can be antimicrobial towards some bacteria).
In culture, the byproducts more-or-less all help the bacteria to survive by providing sulfur, glucose, or other chemicals it needs, but also by acting as an antioxidant compound that binds to a free oxygen (reactive oxygen species) so it doesn’t try to bond with chemicals on the surface of cells and cause them damage (oxidation damage). The byproducts also appear to help the bacteria thrive in acidic culture media which they otherwise can’t survive. When cultured with colon cells and GLR, some of those bacteria and their byproducts reduce inflammation.
The culmination of the past few years of work was to choose two bacterial cultures to try out our idea: that probiotics plus the broccoli sprout diet would help individuals who were not responsive to the diet. Because the gut microbiome, health, and the way that an individual and their microbes respond to diet are all very complicated processes that are specific to each person, it’s easier to test some of these concepts first in the lab or, which we did in early January, in animal models that mimic disease conditions in humans.
We ran a short trial in mice to find out if our two bacterial cultures that were so successful in the lab would also be effective when put back into the chaotic and competitive ecosystem of the gut. To further challenge our bacteria, we tested their ability to survive and reduce inflammation during a flare up of ulcerative colitis.
Every day for almost two weeks, we weighed each mouse (shown below) to make sure the colitis did not cause too much weight loss. Sue, Alexis, Johanna, and Ashley were all approved to handle the mice, so we were in charge of picking them up to weigh them. This was no easy task – mice are agile!
Each day, we also collected feces from the cages to check for diarrhea, or for blood, which are two symptoms of colitis. Our undergrads Madison and Brian worked tirelessly to tweeze feces into collection tubes, and to use the FOBT cards to check for blood.
We used custom made gelatin cubes filled with probiotic to deliver our treatments. The gelatin stuck to the side of the cages which allowed us to easily see that our mice were consuming their probiotic.
It will take us months to process some of the samples we collected which are the most cost-effective to run, and the rest will have to wait in the freezer until we receive more funding (which could take months or years as the changes to the federal funding system have doubled the time it takes for proposals to be reviewed and the ~5-20% of accepted projects to receive funding). We collected >500 fecal samples (each with 5 – 10 pellets/sample), 200 gut samples, 100 intestinal tissue samples, and 50 blood samples! To help maximize the benefits of this experiment and use all parts of these mice we also collected samples for a course at UMaine which teaches pre-medical, pre-veterinary, nursing, biology, and other health-focused students how to make and read tissue slides, to better understand anatomy, physiology, developmental biology, and health.
Still, we gained valuable data already, and the experiment provided a unique opportunity for students to receive hands-on-training for evaluating disease intensity using fecal samples, using tissues to make slides for histology, evaluating intestinal damage to tissues, collecting samples using aseptic technique to prevent contaminating them, working safely with microbes, and collaboratively working as a team to advance knowledge of health. Myself and our grad team (Johanna, Alexis, and Ashley) managed the project, and our undergrad team (Madison, Brian, Aaron, and Alexandra) were there to help us label ~1000 tubes for sample collection, and collect hundreds of fecal pellets out of the used bedding so we could track mouse microbes. Undergrads were also able to learn some general mouse care and research facility care from the ‘mouse house’ technician at UMaine, Alexis R. A former UMaine undergrad in the AVS program, Alexis R. manages and cares for a wide variety of animal species and she was instrumental in helping us manage our intensive sample collection schedule.
Johanna, Ashley, Alexis, and Sue put in long hours during the mouse trial to collect samples each day.
This project was made possible by the help of many. Again, we are grateful to Alexis and the UMaine CORE staff who not only support research at specialized facilities but helped us to afford to run our pilot project, to Emma who runs the UMaine Electron Microscopy Lab for teaching students histology and microscopy, to all the undergraduate and graduate students who worked tirelessly to help each other on this project, and to the funding agencies which supporting the lab work that helped us get to this project: the Biomedical Association of Maine (graduate awards), the Crohn’s and Colitis Foundation (graduate awards), the NIH NIDDK, and the USDA.
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.
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.
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.
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!
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 put in long hours during the mouse trial to collect samples each day.Ashley learned how to handle mice on this project. Here she is weighing the first mouse she learned to pick up.
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.
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.
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.
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.
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.
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.
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 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.
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.
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).
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.
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.
“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.
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.
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”
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
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.
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.
The Ishaq Lab 