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.

2024 Year in Review

sueishaqlabLeave a comment

The Ishaq Lab celebrated 5 years at UMaine this fall, which coincided with many achievements for lab members and early tenure for me! 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

  • Some of the Ishaq Lab gathered for a lunch to celebrate recent achievements
  • Lab lunch with Mira Talalay, Sue, and Marissa Kinney
  • Sue Ishaq and Alexis Kirkendall posing for a photo in a stairwell.
    Sue and Alexis
  • Tolu Esther Alaba is standing in front of a science conference poster, smiling, and holding her infant.
    Tolu Esther Alaba at her 2024 CIMM poster.

Ayodeji Olaniyi defended his Master’s of Animal Science on bacteria in scallop hatchery tanks in February, and has been working in lab-based research ever since.

Tolu Alaba defended her PhD in Biomedical Science over the summer, after her first review with the lab was published. She presented her work several times over the year, and continues to collaborate with the lab on several more manuscripts in preparation. Tolu recently began a postdoctoral position at a research lab at Cedars-Sinai, and continues to research how diet can be used to resolve disease.

Marissa Kinney just defended her Master’s of Microbiology a few weeks ago, and is looking for lab-based microbiology research positions here in Maine. She’ll also continue to collaborate with the lab on several manuscripts in preparation.

Johanna Holman advanced from being a PhD student to being a PhD candidate in the Microbiology program, when she passed her comprehensive exam this fall. She presented her work several times this year, and creatively modified her poster to fit a smaller-than-expected board – but it caught a lot of passerby’s attention! This year, Johanna wrote two versions of a research proposal which are under review for federal funding – keep your fingers crossed!

Heather Richard is preparing for her comprehensive exam next month, in order to advance to PhD candidacy in the Ecology and Environmental Sciences program. She’s been analyzing sequencing data from hundreds of samples from salt marsh sediments in Maine to understand how microbial communities affect carbon sequestration.

Lola Holcomb, PhD candidate in the GSBSE program, was featured in UMaine news, and won a graduate student research award from the Bioscience Association of Maine!! Over the next few months, she’ll focus on characterizing candidate anti-inflammatory bacterial species and genes in the gut microbiome, using whole genome sequence data from bacteria we previously isolated during a broccoli sprout diet study. Lola also wrote two different research proposals this year, one of which is still under review, but has accelerated her timeline and is planning to defend her dissertation in April!

Alexis Kirkendall started her first year as a PhD student in the Microbiology Program, but she has already won two research awards: a Student Research Award from the Crohn’s and Colitis Foundation in 2024, and a Graduate Student Research Award from the Bioscience Association of Maine for 2025!! Over the next year, she’ll focus on culturing bacteria that we previously isolated from mice consuming a steamed broccoli sprout diet, to test their capacity to grow amongst the gut pathogen Helicobacter pylori and produce the anti-inflammatory sulforaphane under different conditions.

Ashley Reynolds, PhD student in Food and Human Nutrition program, passed her exam to become a Registered Dietician! In her second year, Ashley has been developing her thesis proposal and is exploring adding a new facet to the lab’s collaborative research on broccoli sprouts by investgiating the effect on inflammation in other parts of the body.

Seven 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, with a few others who joined the lab in spring to complete their Capstone project on other topics. Collectively, the undergraduates contributed to a large-scale bacterial culturing project, a comparative gene project, and the adminstrative/organizational work required to keep a research lab running.

I was awarded tenure this year (I went up a year early)! This means that I am now an Associate Professor on a permanent contract, although I still get reviewed every few years, and will still have to apply for advancement to (full) Professor in the future. I celebrated all year with family, friends, and colleagues!

I also began 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 >37,000 members around the world. I’ll be sharing more of that experience next year, but so far it’s been an exciting opportunity to learn about strategic planning to support microbiological sciences on an international scale.

Publications

We had a quieter year than usual for publications, with two papers being accepted in scientific journals. I was also part of a white paper that recently was published, and we have five manuscripts which have been undergoing peer review for months.

  1. Costigan2, E., Bouchard, D. Ishaq, S.L., MacRae, J.D. 2024. Short-term effects of abrupt salinity changes on aquaculture biofilter performance and microbial communities. Water 16(20), 2911.
  2. Alaba2, T.E., Holman2, J.M., Ishaq, S.L., Li, Y. 2024. Current knowledge on the preparation and benefits of cruciferous vegetables as relates to in vitro, in vivo, and clinical models of Inflammatory Bowel Disease.  Current Developments in Nutrition: 102160.
  3. Weissman, JL, Chappell, C.R., Rodrigues de Oliveira, B.F., Evans, N., Fagre, A.C., Forsythe, D.,  Frese, S.A., Gregor, R., Ishaq, S.L., Johnston, J., Bittu, K.R., Matsuda, S.B., McCarren, S., Ortiz Alvarez de la Campa, M., Roepkw, T.A., Sinnott-Armstrong, N., Stobie, C.S., Talluto, L., Vargas-Muñiz, J., Advancing Queer and Trans Equity in Science (AQTES). Running a queer- and trans-inclusive faculty hiring process. EcoEvoRvix repository 6791, DOI: https://doi.org/10.32942/X2J310

Presentations

We had a more active year for presentations than usual! I was invited to give several guest lectures and seminars, and a group of us were able to travel to Cape Town, South Africa in August for the International Society for Microbial Ecology conference!!

  • Tolu Alaba presenting her research at a conference.
  • Johanna Holman with her ISME poster
  • Lola Holcomb with ISME poster
  • Tolu Esther Alaba is standing in front of a science conference poster, smiling, and holding her infant.
    Tolu Esther Alaba at her 2024 CIMM poster.
  1. Alaba2*, T. Steamed broccoli sprouts alleviated Inflammatory Bowel Disease via increased anti-inflammatory, antioxidant, and gut protective metabolites in DSS-mice. Functional Food Centre Symposium, San Diego, CA. Oct 2, 2024.
  2. Holcomb2*, Lola, Johanna Holman, Molly Hurd, Brigitte Lavoie, Louisa Colucci, Gary M. Mawe, Peter L. Moses, Emma Perry, Allesandra Stratigakis, Tao Zhang, Grace Chen, Suzanne L. Ishaq, Yanyan Li. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. 19th International Symposium on Microbial Ecology (ISME), Cape Town, South Africa, Aug 19, 2024.
  3. Holman2*, Johanna .M., Lola Holcomb, Louisa Colucci, Dorien Baudewyns, Joe Balkan, Grace Chen, Peter L. Moses, Gary M. Mawe, Tao Zhang, Yanyan Li, Suzanne L. Ishaq. Steamed broccoli sprouts alleviate gut inflammation and retain gut microbiota against DSS-induced dysbiosis. 19th International Symposium on Microbial Ecology (ISME), Cape Town, South Africa, Aug 19, 2024.
  4. Kirkendall2*, A., Holman2, J., Kinney2, M., Sharma1, A., Nowak1, L., Adjapong, G., Li, Y., Ishaq, S.L. Characterizing Gut Bacteria Associated with Sulforaphane Production. 19th International Symposium on Microbial Ecology (ISME), Cape Town, South Africa, Aug 19, 2024.
  5. Ishaq, S. Place and Time Matter for Gut Microbes Making Anti-Inflammatories from Broccoli Sprouts. Northern New England Microbiome Symposium. Burlington, VT, June 3, 2024.
  6. Marissa Kinney, Johanna Holman, Alexis Kirkendall, Emelia Tremblay, Mazie Gordon. Using Steamed Broccoli Sprouts to Better Understand Bacterial Glucosinolate Metabolism. UMaine Student Research Symposium, Orono Maine, April 12, 2024.
  7. Holman, J., Holcomb, L., Colucci, L. Baudewyns, D., Balkan, J., Chen. G., Moses, P.,  Mawe, G.M.,  Zhang, T., Li, Y., Ishaq, S.L. Steamed broccoli sprouts alleviate gut inflammation and retain gut microbiota against DSS-induced dysbiosis. UMaine Student Research Symposium, Orono Maine, April 12, 2024.
  8. Holcomb, L., Holman, J., Hurd, M., Lavoie, B., Colucci, L.,Moses, P., Mawe, G.M., Perry, E., Stratigakis, A., Zhang, T., Ishaq, S.L., Li, Y. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. UMaine Student Research Symposium, Orono Maine, April 12, 2024.
  9. Ishaq, S. “Place and time matter for gut microbes making anti-inflammatories from broccoli sprouts”, Institute for Systems Biology, Seattle, WA. March 15, 2024.
  10. Alaba*, T.E., Ishaq, S.L., Li, Y., Zhang, T. “Broccoli sprouts alleviate ulcerative colitis in mice by increasing dietary and microbial metabolites: differential effects in young and adult, male and female mice. 4th CMI International Microbiome Meeting (CIMM), La Jolla, CA, March 12th – 14th, 2024.
  11. Holcomb*, L., Holman, J., Hurd, M., Lavoie, B., Colucci, L., Moses, P., Mawe, G.M., Perry, E., Stratigakis, A., Zhang, T., Ishaq, S.L., Li, Y. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. 4th CMI International Microbiome Meeting (CIMM), La Jolla, CA, March 12th – 14th, 2024.
  12. Ishaq, S. “Place and time matter for gut microbes making anti-inflammatories from broccoli sprouts”, 4th CMI International Microbiome Meeting (CIMM), La Jolla, CA. March 12, 2024. (invited)
  13. Ishaq, S. “Place and time matter for gut microbes making anti-inflammatories from broccoli sprouts”, Oregon State University microbiology departmental series. Corvalis, OR. March 5, 2024.
  14. Interviewed by Mark Martin on the Matters Microbial podcast, “Episode #27: Broccoli Sprouts, Gut Health, and Microbes for All with Sue Ishaq”, Feb 9, 2024.
  15. Ishaq, S. “Place and time matter for gut microbes making anti-inflammatories from broccoli sprouts”, Translational Biobehavioral and Health Disparities Virtual Microbiome Series. Virtual. Feb 2, 2024.
  16. Olaniyi*, A., Ishaq, S. Investigating the activity of bacteria isolated from tank biofilms in a hatchery system for sea scallop, Placopecten magellanicus, larvae. Northeast Aquaculture Conference & Exposition (NACE) and the 43rd Milford Aquaculture Seminar (MAS). Portland, Maine, January 10-12, 2024.
  17. Ishaq, S. Bacterial community trends associated with sea scallop, Placopecten magellanicus, larvae in a hatchery system. Northeast Aquaculture Conference & Exposition (NACE) and the 43rd Milford Aquaculture Seminar (MAS). Portland, Maine, January 10-12, 2024.

I also gave three interviews on podcasts and webinars this year:

  1. “How a rumen microbiologist got into social equity”, ASM Undergraduate and Graduate Student Webinar series, hosted by Ragini Reddyvari, Oct 9, 2024.
  2. “Save the microbes, save the world“, GW Integrative Medicine Podcast, Interviewed by Dr. Leigh Frame, Aug 28, 2024.
  3. “Episode #27: Broccoli Sprouts, Gut Health, and Microbes for All with Sue Ishaq”, Matters Microbial podcast, interviewed by Mark Martin, Feb 9, 2024.

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.

Logo that reads "The Broccoli Project" and shows cartoons of broccoli, a microscope, a bacteria, and a digestive tract.

We concluded the diet intervention trial in which we asked people to eat a large quantity of steamed broccoli sprouts every day for a month, and spent most of the summer and fall creating personalized reports to share data with each participant. We are still processing the samples to generate more data on metabolites and bacterial genes, but we hope to weave that into a manuscript next year.

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! Now that we have identified which bacteria are of interest to us, we can proceed with whole-genome sequencing as part of Lola’s BioME research project, as well as different culturing trials as part of Alexis’ BioME research project.

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.

The first is 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 have a prospective piece under review, and hope to publish our working definition in late 2025.

In July 2025, the Stewardship group, along with the Microbes and Social Equity working group, will be hosting a research summit on microbiome stewardship at UMaine in Orono! The summit will combine presentations from experts with guided group activities which stimulate critical thinking and planning. The goal is for summit attendees to discuss the concept of microbiome stewardship, and contribute to creating a consensus definition of it.

Some of these group activities that I’ve been designing for the Stewardship summit were inspired by the working meeting hosted by the Nova Institute for Health which I’ve attended the past two years in Baltimore as an Invited Faculty Fellow. Their meeting facilitates creative thought on health research, education, policy, and communications, and brings researchers, practitioners, journalists, and artists together to collaborate.

The second group is the newly formed Advancing Queer and Trans Equity in Science (AQTES) working group, which wants to improve the field of research by making it fair and welcoming for everyone. The group coalesced around the writing of a recently published white paper, in which we give suggestions on how to host a job search that is better for everyone. We provide examples and advice on how to write job adverts, create the agenda and atmosphere for the job search, how to make the interview process more accessible for everyone by remembering that we are humans and not robots, and how to support your new faculty. We recently presented these efforts, and hosted a panel discussion on research culture, at the MSE speaker series.

Microbes and Social Equity working group

The MSE group has more than 350 members, and about 150 additional people just subscribed to our newsletter. New this year, we added an elected Board of Directors, who spent much of the year drafted By-Laws for group governance, a Code of Conduct, and the beginnings of a Strategic Plan. In 2025, the MSE group will provide feedback prior to Board votes to enact these.

In 2024, we tried a monthly seminar series instead of weekly, which helped to reduce administrative burden. The series drew >300 live attendees and >1660 registrations, and some of the seminar recordings can be viewed here.

Population Descriptors and the study of Human Microbiomes: Implications for Appropriate Participant Categorization based on recommendations from the NASEM report.
Precision Microbiome for Health
Don’t Stop Believin’: Managing student motivation on the journey from descriptive to mechanism
Linking Plant, Animal, and Human Health in Livestock Systems: a Metabolomics Approach.
The human microbiome and cancer risk: Opportunities for prospective studies
Antimicrobial chemicals, antimicrobial resistance, and the indoor microbiome
What microbes can teach us about the built environment
The PATHOME Study: Leveraging contrasts in urban socio-economic living conditions and pathogen diversity in humans, animals, and the environment to prioritize intervention policy in Kenya
Examining antibiotic resistance in biofilm and planktonic bacterial communities along an urban river
Building multifunctional agricultural landscapes – from microbes to people
Advancing Queer and Transgender Equity in Science (AQTES)

Teaching

This was a busy year for teaching, as I teach 2 courses in the fall and 2 in the spring, which total ~150-180 students per year. I also taught a handful of students lab research for their Capstone projects via independent study courses. Thanks to some strategic changes to the format of some of my courses, I successfully reduced my workload while improving engagement in the courses. For example, in spring 2024, I “flipped the classroom” for AVS 401 Capstone I in which I teach students how to be researchers and write research proposals, which means that many of the lectures were recorded and we used classroom time for active learning through activities and problem-solving.

In fall 2024, I added an asynchronous section to my AVS 254 Intro to Animal Microbiomes course, allowing for a record 94 students to enroll while maintaining a smaller in-person section with lots of in-class activities and problem solving. I plan to take a sabbatical in fall 2025, and for my teaching professional development goals, I plan to flip that classroom as well, which will take months of revisions to the existing lectures and assignments.

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: 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 >5,150 across those platforms and twitter, facebook, instagram, linked in, mastodon, and subscribers to my blog. The website attracted >10,000 visitors and >18,000 views, bringing it to >64,000 total visitors and >118,000 total views since 2016.

In 2024, I wrote >22,000 words across 53 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.

Looking ahead to 2025

The lab already has a lot planned for 2025! Lola intends to defend her PhD dissertation and graduate, Heather will be taking her comprehensive exam to advance to candidacy and likely Ashley will as well. Undergraduates Benjamin Hunt, Timothy Hunt, and Emelia Tremblay will all be graduating in May and going on to bigger and brighter opportunities. We expect at least three 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 presenting my work in February at the University of Vermont as part of a research symposium session honoring collaborations with the late Dr. Gary Mawe, as well as part of the Distinguished Lectures in Microbiology Series at the University of Wisconsin -Madison. In May I’ll be heading to San Diego to be part of a Microbe Specialist Group at a special meeting to make recommendations on conservation to the Species Survival Commission (SSC) of the International Union for Conservation of Nature (IUCN). In June I’ll be heading to LA to attend the annual Microbe meeting of the American Society for Microbiology, and in July I’ll be hosting the Microbiome Stewardship summit at UMaine.

Other than all that, I’m looking forward to a spring semester that is less hectic than my fall semesters always are, some time off this summer, and sabbatical in the fall which will provide teaching-release so I can focus on professional development.

Happy New Year!

MSE seminar today on “Advancing Queer and Transgender Equity in Science (AQTES)”

sueishaqlabLeave a comment
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, 2024, once a month on a Friday, 12:00 – 14:00 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 UMaine Cultural Affairs/Distinguished Lecture Committee.

Register here for free!

“Advancing Queer and Transgender Equity in Science (AQTES)“

Presented by Dr. JL Weissman and other members of the Advancing Queer and Transgender Equity in Science (AQTES) working group

Dec 20, 2024 12:00 PM Eastern Standard Time

Jackie Lee “JL” Weissman (they/she) is an Assistant Professor at Stony Brook University starting Fall 2024. Her research examines how microbes survive and thrive across diverse environments. She develops new tools to infer what microbes are doing and can do from DNA sequences captured directly from the environment (“metagenomes”), aiming to improve the representation of microbially-mediated biogeochemical cycles in global climate models. She also has a special interest in using a combination of comparative genomics, population genetics, and mathematical models to understand the ancient and ongoing battle between microbes and their viruses. She believes all students, with supportive training and mentorship, can become highly-capable computational biologists, and loves to show students how a little coding can go a long way.

The newly-formed group, Advancing Queer and Trans Equity in Science (AQTES), wants to improve the field of research by making the hiring process fair and welcoming for everyone. No matter what your personal identity is, we can all agree that fair and unbiased job searches are critical to hiring the best talent. But, sometimes a poorly-organized job search prevents the people with the best talent from applying at all.

In our white paper, we give suggestions on how to host a job search that is better for everyone. We provide examples and advice on how to write job adverts, create the agenda and atmosphere for the job search, how to make the interview process more accessible for everyone by remembering that we are humans and not robots, and how to support your new faculty.

Citation for the paper: Weissman, JL, Chappell, C.R., Rodrigues de Oliveira, B.F., Evans, N., Fagre, A.C., Forsythe, D.,  Frese, S.A., Gregor, R., Ishaq, S.L., Johnston, J., Bittu, K.R., Matsuda, S.B., McCarren, S., Ortiz Alvarez de la Campa, M., Roepkw, T.A., Sinnott-Armstrong, N., Stobie, C.S., Talluto, L., Vargas-Muñiz, J., Advancing Queer and Trans Equity in Science (AQTES). 2024. Running a queer- and trans-inclusive faculty hiring process. EcoEvoRvix repository 6791.

Perspective piece introducing the paper:  Weissman JL, Chappell CR, Francesco Rodrigues de Oliveira B, Evans N, Fagre AC, Forsythe D, et al. (2024) Queer- and trans-inclusive faculty hiring—A call for change. PLoS Biol 22(11): e3002919.

Logo designed by Alex Guillen

Marissa Kinney defended her master’s thesis on glucosinolate metabolism by gut bacteria!

sueishaqlabLeave a comment

Lab rockstar, Marissa Kinney, successfully defended her master’s thesis today!!! After a well-earned holiday break, Master Kinney is pursuing a career in biomedical/microbiological research.

Marissa Kinney

Marissa was Master of Science student in Microbiology, and a researcher in the One Health and the Environment program, both of which are prestigious graduate programs at UMaine, from Jan 2023 – Dec 2024. She loves learning and bench microbiology, and she employed these passions on multiple lab projects investigating the bacteria which transform glucoraphanin in broccoli sprouts into the anti-inflammatory sulforaphane in the gut. The focus of her time has been to develop new lab protocols, refine existing ones and make them easier for new lab members to learn, and to share her expertise by teaching other students in the lab. She’s excelled at these objectives so well, that in the past two years many people assumed she was a Lab Manager rather than a student.

Marissa has been extremely productive in the last two years: in her first three months she contributed lab work to two publications on broccoli sprout diets in mouse models of Inflammation Bowel Disease in 2023, and has since contributed to another manuscript currently in review on glucoraphanin supplements and gut microbiome changes in people, and two more manuscripts in preparation on culturing gut microbiota, and a broccoli sprout diet in people. It’s no surprise that Marissa has been an author on so many papers in so little time — she led a publication when she was an undergraduate! You can check her Google Scholar page for more info on these papers. Marissa has also presented this work on campus at the UMaine Student Research Symposium twice, as well as attended conferences for the American Society for Nutrition and the American Society for Microbiology for professional development.

  • Marissa Kinney presenting research.
  • The Ishaq Lab at Boda Borg in Boston, summer 2023. We are showing how many quests we completed.
  • Lab lunch with Mira Talalay, Sue, and Marissa Kinney

Previous to being in the lab, Marissa completed her undergraduate at the University of Maine in 2021, earning a BS in Microbiology and a BS in Cellular/Molecular Biology. She devoted a large portion of her time in undergrad to research in the laboratories of Dr. Julie Gosse and Dr. Edward Bernard. After graduating, she worked in the field of public health at UMaine’s Margaret Chase Smith Policy Center, collecting and processing data about violent and drug-related deaths in Maine. While her role at the Center was one she loved dearly, she felt a big pull towards laboratory work and academic research, and her graduate work enforced this passion. Marissa has been a core member of the lab, and we’ll miss her!! She plans to pursue a research career here in Maine after defending and enjoying a well-earned vacation.

USING BROCCOLI SPROUT DIETS TO UNDERSTAND GUT BACTERIAL GLUCOSINOLATE METABOLISM TO RESOLVE INFLAMMATORY BOWEL DISEASE

Abstract

Globally, millions of people have been diagnosed with a type of inflammatory bowel disease (IBD). These diseases cause dysfunction of the gastrointestinal (GI) tract, resulting in a wide range of symptoms that create a disruption in overall health. Research has suggested that diet and the microbial community composition of the gut microbiome play a significant role in regulating gastrointestinal inflammation. Specifically, studies have shown that diets high in cruciferous vegetables, such as broccoli, are associated with a reduction in gastrointestinal inflammation. Glucoraphanin is a compound present in broccoli that can be metabolized by gut bacteria to become an anti-inflammatory compound known as sulforaphane. Our initial research showed that the administration of a broccoli sprout diet to mouse models for Crohn’s disease and ulcerative colitis, two major types of IBD, yields inflammation reduction and symptom resolution. For these trials, fecal samples obtained from different sections of the mouse bowel were tested for presence of glucoraphanin-metabolizing genes present in a common gut bacteria, Bacteroides thetaiotaomicron (B. theta). Glucoraphanin conversion is higher and more reliable in mice than in people, however mouse models are not perfect representatives of humans. Hoping to understand the impacts of broccoli sprouts on the human gut microbiome, fecal samples were obtained from healthy individuals who consumed broccoli sprouts for 28 consecutive days, as long-term diet interventions are needed to meaningfully change gut microbial communities. In a separate trial conducted by the scientists at Brassica Protections Product, fecal samples were collected from people who were administered a single dietary supplement containing a high dose of glucoraphanin with and without plant-sourced myrosinase, as a means of evaluating the effectiveness of glucoraphanin conversation which was or was not reliant on gut microbiota, respectively. These samples were analyzed for glucoraphanin metabolizing genes from B. theta and other commensal gut bacteria. Data collected from these human trial experiments aided in understanding the impacts of a whole food broccoli sprout diet and supplementation of glucoraphanin on the bacterial community composition of the gut microbiota. Additionally, this work will help grow and strengthen the current knowledge on broccoli as an anti-inflammatory and the variabilities present in the gut microbiomes of humans.

Alice Hotopp prepares for her dissertation defense on feather melanism, adapation, and feather microbes!

sueishaqlabLeave a comment

Alice Hotopp will defend her PhD dissertation this Thursday! The presentation is open to the public, and the zoom link is here. Alice is in the Ecology and Environmental Sciences program, and she is advised by Drs. Kristina Cammen and Brian Olsen. She has been an affiliate of the Ishaq Lab for several years, as some of her work investigated the bacterial and fungal communities on feathers of several species of salt marsh sparrows, and she performed much of the data analysis on a study identifying bacteria that can be transferred by nemotodes to ants.

Hotopp-Defense-FlyerDownload
Alice Hotopp

Alice Hotopp, M.S.

Alice is a PhD candidate in Ecology and Environmental Sciences, co-advised by Drs. Kristina Cammen and Brian Olsen. Alice is part of the Genomic Ecology of Coastal Organisms (GECO) research group, which studies the genomic basis of adaptation in sparrow species inhabiting tidal salt marshes along the Atlantic coast of North America. Alice’s research focuses on understanding potential evolutionary drivers of plumage coloration, such as plumage microbial communities, in tidal marsh sparrows. 

Papers published with the Ishaq Lab:

Hotopp AM, Olsen BJ, Ishaq SL, Frey SD, Kovach AI, Kinnison MT, Gigliotti FN, Roeder MR, Cammen KM (2024) Tidal marsh sparrow plumage microorganism communities. iScience. 27: 108668.

Ishaq SL, Hotopp A, Silverbrand S, Dumont JE, Michaud A, MacRae JD, Stock SP, Groden E. Bacterial transfer from Pristionchus entomophagus nematodes to the invasive ant Myrmica rubra and the potential for colony mortality in coastal Maine. iScience. 2021 May 29;24(6):102663.

Lola Holcomb won a student research award from the Bioscience Association of Maine!!

sueishaqlabLeave a comment

Congratulations to Lola Holcomb, PhD candidate in the Graduate School for Biomedical Sciences and Engineering program, for winning a graduate student research award from the Bioscience Association of Maine!!

Over the next few months, she’ll focus on characterizing candidate anti-inflammatory bacterial species and genes of the gut microbiome, using whole genome sequence data from bacteria we previously isolated during a broccoli sprout diet study. This is part of Lola’s larger PhD project investigating which bacteria produce sulforphane in the gut, how they do it, and under which circumstances. It complements the collective lab research on how broccoli sprouts and gut microbes can be used to resolve Inflammatory Bowel Disease.

Portrait of Lola Holcomb, wearing a block sweater on a beach at sunset

Lola Holcomb, B.S.

Doctorate of Philosophy candidate, Biomedical Science

Lola entered as a rotating first-year GSBSE student in March 2022, and declared the Ishaq Lab her dissertation lab soon after.  Troubled with indecisiveness and the desire to research, well, everything, she quickly found that using bioinformatics and big data as a lens to study microbial ecology (and in time, its relation to social equity) allowed her to do the kind of meaningful interdisciplinary research she’s always wanted to do.  Lola is currently working on 16s data analysis for other ongoing lab projects, comparing gut microbiomes of mouse models of Inflammatory Bowel Disease with broccoli as a dietary treatment.  Lola is currently doing 16S data analysis for ongoing lab projects and developing a metagenomic analysis workflow to compare gut microbiomes of mouse models of Inflammatory Bowel Disease with broccoli as a dietary treatment. In addition to research, she instructs a graduate-level Genetics course, tutors several Biology undergraduate students, and serves as a GSBSE senator in the Graduate Student Government here at UMaine. 

Google Scholar page.

Alexis Kirkendall won a student research award from the Bioscience Association of Maine!!

sueishaqlabLeave a comment

Congratulations to Alexis Kirkendall, PhD student in the Microbiology Program, for winning a graduate student research award from the Bioscience Association of Maine!!

Over the next year, she’ll focus on culturing bacteria that we previously isolated from mice consuming a steamed broccoli sprout diet, to test their capacity to grow amongst the gut pathogen Helicobacter pylori and produce the anti-inflammatory sulforphane under different conditions. This will be part of Alexis’ larger PhD project investigating which bacteria produce sulforaphane in the gut, how they do it, and under which circumstances. It complements the collective lab research on how broccoli sprouts and gut microbes can be used to resolve Inflammatory Bowel Disease.

Alexis Kirkendall

Doctor of Philosophy student, Microbiology

Alexis is from Ohio and initially joined the lab in 2022 when she was majoring in Biology at Heidelberg University, through the Summer 2022 REU, during which she divided her time researching Cryptosporidium in cows, helping in the MSE Symposium, and aiding in the Camel Rumen Microbiome Project. Alexis continued her work remotely, and returned to Maine in summer 2023 as a research assistant for several projects related to gut microbes, diet, and Inflammatory Bowel Disease. Her research interests are in genetics and she has a love for the fascinating world of microbes.

She returned in January 2024 as a graduate student in the Microbiology program!

 

MSE seminar today: “Building multifunctional agricultural landscapes – from microbes to people.”

sueishaqlabLeave a comment

Events will be hosted January – December, 2024, once a month on a Friday, 12:00 – 14:00 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 UMaine Cultural Affairs/Distinguished Lecture Committee.

Register here for one or all speakers for free!

“Building multifunctional agricultural landscapes – from microbes to people”

Dr. Aidee Guzman, PhD.

Dec 6, 2024 12:00 PM Eastern Standard Time. This event has passed, watching the recording here.

Dr. Aidee Guzman is an assistant professor at Stanford University in the Department of Biology in the Ecology and Environmental Science group. Her research group examines agroecological approaches that could harness biodiversity and ecosystem functioning for improved agricultural resilience. Specifically, they investigate how agricultural management impacts biotic interactions (e.g. between plants, insects, and soil microbes) across scales (e.g. shifts in community structure, cascading changes in ecosystem functioning). The overarching goal of her research program is to support farmers, especially those who are historically underserved, through research, education, and outreach that builds on their innovations and demonstrates ecological pathways to agricultural resilience. 

Lab website here.

Logo designed by Alex Guillen

Marissa Kinney set to defend her master’s thesis on glucosinolate metabolism by gut bacteria!

sueishaqlabLeave a comment

Lab rockstar, Marissa Kinney, is set to defend her Master’s of Science thesis in Microbiology on Wednesday, December 18th!! The thesis abstract is below.

You can register here for the publicly available seminar portion from 1 – 2 pm ET on Zoom

Marissa Kinney

Marissa has been a Master of Science student in Microbiology, and a researcher in the One Health and the Environment program, both of which are prestigious graduate programs at UMaine, for the last two years. She loves learning and bench microbiology, and she employed these passions on multiple lab projects investigating the bacteria which transform glucoraphanin in broccoli sprouts into the anti-inflammatory sulforaphane in the gut. The focus of her time has been to develop new lab protocols, refine existing ones and make them easier for new lab members to learn, and to share her expertise by teaching other students in the lab. She’s excelled at these objectives so well, that in the past two years many people assumed she was a Lab Manager rather than a student.

Marissa has been extremely productive in the last two years: in her first three months she contributed lab work to two publications on broccoli sprout diets in mouse models of Inflammation Bowel Disease in 2023, and has since contributed to another manuscript currently in review on glucoraphanin supplements and gut microbiome changes in people, and two more manuscripts in preparation on culturing gut microbiota, and a broccoli sprout diet in people. It’s no surprise that Marissa has been an author on so many papers in so little time — she led a publication when she was an undergraduate! You can check her Google Scholar page for more info on these papers. Marissa has also presented this work on campus at the UMaine Student Research Symposium twice, as well as attended conferences for the American Society for Nutrition and the American Society for Microbiology for professional development.

  • Marissa Kinney presenting research.
  • The Ishaq Lab at Boda Borg in Boston, summer 2023. We are showing how many quests we completed.
  • Lab lunch with Mira Talalay, Sue, and Marissa Kinney

Previous to being in the lab, Marissa completed her undergraduate at the University of Maine in 2021, earning a BS in Microbiology and a BS in Cellular/Molecular Biology. She devoted a large portion of her time in undergrad to research in the laboratories of Dr. Julie Gosse and Dr. Edward Bernard. After graduating, she worked in the field of public health at UMaine’s Margaret Chase Smith Policy Center, collecting and processing data about violent and drug-related deaths in Maine. While her role at the Center was one she loved dearly, she felt a big pull towards laboratory work and academic research, and her graduate work enforced this passion. Marissa has been a core member of the lab, and we’ll miss her!! She plans to pursue a research career here in Maine after defending and enjoying a well-earned vacation.

USING BROCCOLI SPROUT DIETS TO UNDERSTAND GUT BACTERIAL GLUCOSINOLATE METABOLISM TO RESOLVE INFLAMMATORY BOWEL DISEASE

Abstract

Globally, millions of people have been diagnosed with a type of inflammatory bowel disease (IBD). These diseases cause dysfunction of the gastrointestinal (GI) tract, resulting in a wide range of symptoms that create a disruption in overall health. Research has suggested that diet and the microbial community composition of the gut microbiome play a significant role in regulating gastrointestinal inflammation. Specifically, studies have shown that diets high in cruciferous vegetables, such as broccoli, are associated with a reduction in gastrointestinal inflammation. Glucoraphanin is a compound present in broccoli that can be metabolized by gut bacteria to become an anti-inflammatory compound known as sulforaphane. Our initial research showed that the administration of a broccoli sprout diet to mouse models for Crohn’s disease and ulcerative colitis, two major types of IBD, yields inflammation reduction and symptom resolution. For these trials, fecal samples obtained from different sections of the mouse bowel were tested for presence of glucoraphanin-metabolizing genes present in a common gut bacteria, Bacteroides thetaiotaomicron (B. theta). Glucoraphanin conversion is higher and more reliable in mice than in people, however mouse models are not perfect representatives of humans. Hoping to understand the impacts of broccoli sprouts on the human gut microbiome, fecal samples were obtained from healthy individuals who consumed broccoli sprouts for 28 consecutive days, as long-term diet interventions are needed to meaningfully change gut microbial communities. In a separate trial conducted by the scientists at Brassica Protections Product, fecal samples were collected from people who were administered a single dietary supplement containing a high dose of glucoraphanin with and without plant-sourced myrosinase, as a means of evaluating the effectiveness of glucoraphanin conversation which was or was not reliant on gut microbiota, respectively. These samples were analyzed for glucoraphanin metabolizing genes from B. theta and other commensal gut bacteria. Data collected from these human trial experiments aided in understanding the impacts of a whole food broccoli sprout diet and supplementation of glucoraphanin on the bacterial community composition of the gut microbiota. Additionally, this work will help grow and strengthen the current knowledge on broccoli as an anti-inflammatory and the variabilities present in the gut microbiomes of humans.

Dr. Alaba begins a postdoc position in the Michelsen Lab at Cedars-Sinai!

sueishaqlab1 Comment

The Ishaq Lab congratulates Dr. Tolu Alaba on accepting a postition as Postdoctoral Researcher at Cedars-Sinai!!! Tolu will be working in Dr. Michelsen’s Lab which focuses on exploring immune pathways contributing to Inflammatory Bowel Disease-related fibrosis, and Cedars-Sinai is a non-profit organization for healthcare research, education, and services. This position is in line with Tolu’s career goals of using nutrition to influence health.

Tolu Esther Alaba is standing in front of a science conference poster, smiling, and holding her infant.
Tolu Esther Alaba at her 2024 CIMM poster.
Tolu performing metabolomics at UC Irvine during her PhD.
Tolu performing metabolomics at UC Irvine during her PhD.
Tolu presenting at a Functional Food Conference in 2024.

White paper and perspective published on “Running a queer- and trans-inclusive faculty hiring process”!!

sueishaqlabLeave a comment

I’m delighted to announce the public release of a white paper on queer- and trans-inclusive faculty hiring practices, and a perspective piece introducing it!! This is the culmination of months of writing by an international group of talented scientists led by Dr. JL Weissman, and I was honored to participate in these and future efforts from the group.

The newly-formed group, Advancing Queer and Trans Equity in Science (AQTES), wants to improve the field of research by making the hiring process fair and welcoming for everyone. No matter what your personal identity is, we can all agree that fair and unbiased job searches are critical to hiring the best talent. But, sometimes a poorly-organized job search prevents the people with the best talent from applying at all.

In our white paper, we give suggestions on how to host a job search that is better for everyone. We provide examples and advice on how to write job adverts, create the agenda and atmosphere for the job search, how to make the interview process more accessible for everyone by remembering that we are humans and not robots, and how to support your new faculty.

Running a queer- and trans-inclusive faculty hiring process.

Authors

Weissman, JL, Chappell, C.R., Rodrigues de Oliveira, B.F., Evans, N., Fagre, A.C., Forsythe, D.,  Frese, S.A., Gregor, R., Ishaq, S.L., Johnston, J., Bittu, K.R., Matsuda, S.B., McCarren, S., Ortiz Alvarez de la Campa, M., Roepkw, T.A., Sinnott-Armstrong, N., Stobie, C.S., Talluto, L., Vargas-Muñiz, J., Advancing Queer and Trans Equity in Science (AQTES).

Abstract

Queer and transgender scientists face documented systemic challenges across the sciences, and therefore have a higher attrition rate than their peers. Recent calls for change within science have emphasized the importance of addressing barriers to the success and retention of queer and trans scientists to create a more inclusive, equitable, and just scientific establishment. Crucially, we note these calls come primarily from early career researchers; relatively few queer and trans scientists have passed through the gauntlet of the faculty job search to become faculty ourselves, which is typically key to long-term persistence in academia. Our lack of representation creates a self-reinforcing cycle in which queer and trans trainees do not see our needs considered in established processes and power structures. Moreover, this status quo has historically been and continues to be harmful, disproportionately impacting those of us who have multiple intersecting marginalized identities. Here, we provide concrete guidance to search committees to support queer and trans candidates throughout the faculty selection process based on our personal experiences as early career scientists who have been on the job market.

Graphics in the post and the article created by Callie R. Chappell.

Citations

Citation for the paper: Weissman, JL, Chappell, C.R., Rodrigues de Oliveira, B.F., Evans, N., Fagre, A.C., Forsythe, D.,  Frese, S.A., Gregor, R., Ishaq, S.L., Johnston, J., Bittu, K.R., Matsuda, S.B., McCarren, S., Ortiz Alvarez de la Campa, M., Roepkw, T.A., Sinnott-Armstrong, N., Stobie, C.S., Talluto, L., Vargas-Muñiz, J., Advancing Queer and Trans Equity in Science (AQTES). 2024. Running a queer- and trans-inclusive faculty hiring process. EcoEvoRvix repository 6791.

Perspective piece introducing the paper:  Weissman JL, Chappell CR, Francesco Rodrigues de Oliveira B, Evans N, Fagre AC, Forsythe D, et al. (2024) Queer- and trans-inclusive faculty hiring—A call for change. PLoS Biol 22(11): e3002919.

This work is being presented at the American Geophysical Union annual meeting in Washington DC in December, in the session on “ED12A: Advances and Progress Toward a More Inclusive, Diverse, Equitable, and Accessible Scientific Community II”.

This work is being presented as a seminar at the Microbes and Social Equity working group virtual seminar series, Dec 20th, 2024. Registration is free but required.