Tag: Updates

2022 Year in Review

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This was year 3 for the Ishaq Lab at UMaine, and we celebrated all of 2022 with new students, new projects, new funding, and exciting results! Here are some highlights, but you can check out previous blog posts in the archives for more detail. As per usual, I have divided the summary into sections: Team, Research, Publications, Presentations, MSE, Teaching, Website, and looking to the year ahead.

Team

Lacy Mayo, Keagan Rice, and Sydney Shairculturing.
Sarah Hosler, Johanna Holman, and Emily Wissel presenting at ASM Microbe.
Gloria Adjapong extracting hundred of DNA samples.
Sydney Shair and Keagan Rice preparing media.
Aaron Williams, Ayodeji Olaniyi, Sydney Shair, and Keagan Rice culturing.
Ayodeji Olaniyi culturing.
Lacy Mayo making media.
Alexis Kirkendall collected samples from calves.
Alexis Kirkendall processing microscope slides.
Sarah Hosler presenting at ASM Microbe.
Ayodeji Olamiyi processing microscope slides.
A graduate student and a faculty member, both in full graduation regalia, posing for a photo in a gymnasium.
Sarah Holser is walking in the UMaine 2022 graduate graduation, as she will be defending her master’s of science thesis this summer.
Alexis Kirkendall processing microscope slides.
Sarah Hosler defending her master’s thesis.
Some of the 2021/2022 Ishaq Lab members. From the left: Maria, Sue, Sarah, and Ayodeji.
Johanna Holman standing at a wooden podium with a white board and a projection screen behind her. Johanna is presenting her master's thesis, and the title slide of the presentation is showing on the screen.
Johanna Holman beginning her master’s defense presentation.
Sue, Lola Holcomb, and Sarah Hosler hanging out in Portland.
Me on the big screen at ASM Microbe.
Johanna Holman at her ASM Microbe 2022 poster
Johanna Holman at her ASM Microbe 2022 poster
Six women sitting at a picnic table eating lunch outside, and smiling at the camera.
Some of the 2021/2022 Ishaq Lab members. From the left: Sophia, Isabelle, Rebecca, Morgan, Natalie, and Sue.

The Ishaq Lab had its first and second graduate student thesis defense this summer, with Sarah Hosler and Johanna Holman passing their defenses in the same week! They both gave hour-long presentations of their work, answered difficult questions from their committees for another hour, and published all their work to date as a thesis. Johanna’s master’s focused on “Prevention of Inflammatory Bowel Disease by Broccoli-sourced and Microbially-produced Bioactives“, and she has continued with Yanyan Li and I to do her PhD on this. Sarah’s thesis was broader; “Weaving an Interdisciplinary Microbiome Career Using Threads From Different Ecosystems“, and she has taken a job at her undergraduate institution coordinating science education and lab experience for high school students. All of the work from their theses is being written up into manuscripts. Johanna’s literature review was recently published, and will have her other two chapters in review soon, discussed more below. Sarah’s literature review is in review, and her chapters are being added to in preparation for submission to review in early 2023.

Early in 2022, two graduate students joined the Ishaq Lab. Lola Holcomb is a PhD student in the Graduate School of Biomedical Science and Engineering, is based in Portland as GSBSE hosts remote students around Maine. Lola has been focusing on data analysis to understand microbes, health, and social equity. She began first as a rotation student for 10 weeks, and it was such a good match that we promptly assigned her to my lab for the next 4-ish years. Ayodeji Olaniyi is a MS student in Animal Science, and has been assisting on several projects to gain lab experience. He most recently has taken over the scallop tank bacterial culturing project this fall for which we have been processing 150 bacterial isolates through over a dozen culturing tests, which results in hundreds of plates and tubes to make, process, and clean every week for the past two months! There has been a team of undergraduates helping us on this project, discussed more below.

The Ishaq Lab has also been host to two visiting researchers who have been cross-training on our protocols while performing their own research. Dr. Alaa Rabee has been visiting for the last six months on a fellowship from the Cultural Affairs and Missions Sector and Ministry of Higher Education and Scientific Research of Egypt, to study fibrolytic microbes from animals and how the microbes could be used to digest plant biomass for energy production. Dr. Gloria Adjapong is a postdoctoral researcher at the UMaine Cooperative Extension Veterinary Diagnostics Laboratory on a two year fellowship, and has been generously lending a hand in the lab to help us with >700 DNA extractions and sequencing library preparations to investigate bacterial communities in scallop hatcheries.

My dog, Izzy, has been dutifully coming to campus this fall to attend classes and entertain and calm the students, distract Zoom meetings by trying to climb out the window behind me, and help catalogue all the squirrels on campus.

This year, the Ishaq lab said hello as well as good-bye to students, as we have been around long enough that students are matriculating (graduating) out and moving on to the next stage of their life. Sarah Hosler defended her master’s thesis and is currently developing and hosting high school research programs at Albright College. Undergraduates Rebecca French, Morgan Rocks, Natalie Sullivan, Sophia S., and Izzy S. graduated in May and went on to vet school, lab research, animal medical care, and more. Ellie Pelletier is graduating in May, but has completed her research project and all but one of her courses early so we are counting her as outgoing.

Publications

A stack of papers facedown on a table.

We had a productive year for peer-reviewed journal publications – with 7 published! Several of these have been in development since prior to 2022, several are the first publications for students, and all of which are thanks to my fabulous research collaboration team that now spans the globe. There are a handful more papers in peer review at scientific journals, and others which are in preparation and which we hope to submit for peer review in 2023. Below; 1 undergraduate student I mentored, 2 graduate student I mentored for this project

  1. Ishaq, S.L., Turner, S.M., Lee1, G., Tudor, M.S., MacRae, J.D., Hamlin, H., Bouchard, D. 2022. Warmer water temperature and epizootic shell disease reduces diversity but increases cultivability of bacteria on the shells of American Lobster (Homarus americanus). In review, preprint available.
  2. Hosler2, S., Kamath, P.L., Ishaq, S.L. 2022.  A review of technological advances and gaps in detecting and understanding Cryptosporidium protozoan parasites in ruminant livestock. In review.
  3. Four more are on the cusp of submission for review!

  1. Holman2, J., Hurd, M., Moses, P.,  Mawe, G.,  Zhang, T., Ishaq*, S.L., Li*, Y. 2022. Interplay of Broccoli/Broccoli Sprout Bioactives with Gut Microbiota in Reducing Inflammation in Inflammatory Bowel Diseases. Journal of Nutritional Biochemistry. * contributed equally
  2. Ouverson2, T., Boss, D., Eberly, J., Seipel, T.,  Menalled, F.D., Ishaq, S.L. 2022. Soil  bacterial community response to cover crops, cover crop termination, and predicted climate conditions in a dryland cropping system. Frontiers in Sustainable Food Systems. 911199.
  3. Ishaq, S.L., Wissel2, E.F., Wolf, P.G., Grieneisen, L., Eggleston, E.M., Mhuireach, G., Friedman, M., Lichtenwalner, A., Otero Machuca, J.,  Weatherford Darling, K.,  Pearson, A., Wertheim, F.S., Johnson, A.J., Hodges, L., Young, S., Nielsen, C.C., Kozyrskyj, A.L.,  MacRae, J.D., McKenna Myers, E., Kozik, A.J., Tussing-Humphreys, L.M., Trujillo, M., Daniel, G.A., Kramer, M.R., Donovan, S.M., Arshad 1, M., Balkan1, J., Hosler2, S. 2022. Designing the Microbes and Social Equity Symposium, a novel interdisciplinary virtual research conference based on achieving group-directed outputs. Challenges, 13(2), 30.
    • Invited contribution to Challenges, the journal for the inVIVO Planetary Health research group.
  4. Sepiel, T. Ishaq, S.L., Larson, C., Menalled, F. 2022. Weed communities in winter wheat: responses to cropping systems and predicted warmer and drier climate conditions.  Sustainability 14(11), 6880.
  5. Ishaq, S.L., Turner, S.M., Tudor, M.S., MacRae, J.D., Hamlin, H., Kilchenmann, J., Lee1, G., Bouchard, D. 2022. Many questions remain unanswered about the role of microbial transmission in epizootic shell disease in American lobsters (Homarus americanus). Frontiers in Microbiology 13: 824950.
    • Invited contribution to special collection: The Role of Dispersal and Transmission in Structuring Microbial Communities
    • This is the first all-female author team I have published with.
  6. Rabee, A.E., Sayed Alahl, A.A., Lamara, M., Ishaq, S.L. 2022. Fibrolytic rumen bacteria of camel and sheep and their applications in the bioconversion of barley straw to soluble sugars for biofuel production. PLoS ONE 17(1): e0262304. 
    • Impact 3.24.
    • Dr. Rabee will be joining my lab as a Visiting Research in 2022.
  7. Robinson, J.M., Redvers, N., Camargo, A., Bosch, C.A., Breed, M.F., Brenner, L.A., Carney, M.A., Chauhan, A., Dasari, M., Dietz, L.G., Friedman, M., Grieneisen, L., Hoisington, A.J., Horve, P.F., Hunter, A., Jech, S., Jorgensen, A., Lowry, C.A., Man, I., Mhuireach, G., Navarro-Pérez, E., Ritchie, E.G., Stewart, J.D., Watkins, H., Weinstein, P., and Ishaq, S.L. 2022. Twenty important research questions in microbial exposure and social equity. mSystems 7(1): e01240-21. 

Editorials published

  1. Ishaq, S., and Gilbert, J. Introducing the “Microbiomes and Social Equity” Special Collection. mSystems Aug 29, 2022.

Presentations

The Ishaq lab and our collaborators gave in-person and virtual presentations this year to scientific audiences, to students and faculty as guest seminars, and as media/news interviews. Students Sarah Hosler, Johanna Holman, Lola Holcomb, Alice Hotopp, Alexis Kirkendall Rebecca French, and Ellie Pelletier gave or contributed to presentations in 2022.

  1. Kirkendall1*, A., Ishaq, S. Taking on Multiple Research Projects in a NSF Research Experience for Undergraduates (REU) Summer Program as a Disabled Undergraduate Student. Annual Biomedical Research Conference For Minoritized Scientists (ABRCMS) annual meeting, Anaheim, CA, November 9-12, 2022.
  2. Hotopp*2, A., Ishaq, S., Frey, S., King, B., Kinnison, M., Kovach, A., Olsen, B., Cammen, K. 2022. Microbial communities of tidal marsh sparrow plumage. Association of Field Ornithologists conference, Plymouth, MA, October 17 – 21, 2022.
  3. Wissel*2, E., Holman*2, J., Hosler*2, S., Ishaq, S. Microbes and Social Equity: what is it and how do we do it? Part of Track Hub: ‘Field Work & DEI Part 1: Fostering Equitable Partnerships with the Communities in Your Field Work Location’. American Society for Microbiology (ASM) Microbe 2022, Washington, DC (USA), June 9-13, 2022.
  4. Holman, J. M., S. Ishaq, Y. Li, T. Zhang, G. Mawe, L. Colucci, J. Balkan. Prevention of Inflammatory Bowel Disease by Broccoli Sourced and Microbially Produced Bioactives.  American Society for Microbiology (ASM) Microbe 2022, Washington, DC (USA), June 12, 2022.
  5. Hosler2*, S., Grey, E., Dankwa, A., Perry, J., Bowden, T., Beal, B., Ishaq, S. Initial descriptions of  the microbes of farmed Atlantic sea scallop (Placopecten magellanicus) veligers and rearing tanks. American Society for Microbiology Microbe 2022 meeting. Washington, D.C.. June 9-13, 2022.
  6. Hosler2*, S., Grey, E., Ishaq, S. Comparing the microbiome of wild and farmed Atlantic sea scallop (Placopecten magellanicus) veligers. Northeast Aquaculture Conference & Exposition (NACE) and the 41st Milford Aquaculture Seminar (MAS). Portland, Maine. POSTPONED to April 27-28, 2022
  7. Ishaq, S., Li, Y., Holman*2, J., Zhang, T., Chen, G. “Biogeography may be key to microbial anti inflammatory production using dietary precursors.” Maine Biological and Medical Sciences Symposium, Bar Harbor, ME, April 22-23, 2022. (invited, canceled due to time conflict, graduate student presented in my place)
  8. French1*, R., Beale, J., Ishaq, S. Abstract 0402. Climate Change Affects Wild Mammal Ranges and Health; Will That Also Affect Infectious Disease Exposure Risk at Maine Farms? UMaine Student Symposium (virtual presentation). April 15, 2022.
  9. Holcomb2*, Coffman, J., Harrison, B., Tucker, K., Ishaq, S. Abstract 1080. An Overview of Three Biomedical Science Projects across Three Research Institutes. UMaine Student Symposium (virtual presentation). April 15, 2022.
  10. Hosler2*, S., Grey, E., Dankwa, A., Perry, J., Bowden, T., Beal, B., Ishaq, S. Abstract 0816. Initial descriptions of the microbes of farmed Atlantic sea scallop (Placopecten magellanicus) veligers and rearing tanks. UMaine Student Symposium (virtual presentation). April 15, 2022.
  11. Pelletier1*, E., Taylor, T., Ishaq, S. Abstract 830. Assessing the Veterinary Needs of Rural Maine and Implementing an Effective Management Plan. UMaine Student Symposium (poster presentation). April 15, 2022.
  12. Ishaq, S. “Microbes at the nexus of environmental, biological, and social research.” Iowa State University Spring Microbiology Graduate Student Organization retreat. (virtual). April 14, 2022 (invited co-plenary).
  13. Ishaq*, S., Li, Y., Holman2, J., Zhang, T., Mawe, G., Hurd, M., Lavoie, B. Baudewyns1, D., Colucci1, L., Balkan1, J., Chen, G, Moses, P. “Biogeography may be key to microbial anti inflammatory production using dietary precursors.”  Congress of Gastrointestinal Function (CGIF), virtual. April 11 – 13, 2022.
  14. Ishaq*, S., Li, Y., Holman2, J., Zhang, T., Mawe, G., Hurd, M., Lavoie, B. Baudewyns1, D., Colucci1, L., Balkan1, J., Chen, G, Moses, P. “Biogeography may be key to microbial anti inflammatory production using dietary precursors.”  Dartmouth Molecular Microbiology and Pathogenesis (M2P2), February 24 – 25, 2022. (invited)
  15. Ishaq, S. ​”Microbes at the nexus of environmental, biological, and social research.” 2nd Rhode Island Microbiome Symposium, virtual, University of Rhode Island Kingston, RI, January 14, 2022. (invited plenary)
  16. Ishaq, S. “Moose rumen microbes and you.” The Wildlife Society Nutritional Ecology Working Group Webinar series, (virtual), March 9, 2022.
  17. Ishaq, S. “Microbes at the nexus of environmental, biological, and social research” The Microbes and Social Equity 2022 speaker series, virtual, University of Maine and the Microbes and Social Equity working group. January 19, 2022.

Media Interviews

  1. “Can broccoli sprouts be used to treat IBD? UMaine researchers investigate”, Carly D’Eon, News Center Maine, Nov 22, 2022.
  2. “UMaine researchers studying whether broccoli sprouts can help prevent and treat inflammatory bowel disease”, Marcus Wolf, UMaine News.
  3. “Egyptian scientist visits UMaine“, Alaa Rabee and Sue Ishaq, interview by Matthew Jaroncyk, Fox 22 Bangor, Jun 27, 2022.
  4. Featured as a woman in microbiome science for Women’s History Month by the National Microbiome Data Collaborative, Twitter, Mar 30, 2022
  5. Interviewed for “Invisible Friends”, Dr. Jake Robinson, book in production, 2022.

Research

This year has seen varied topics come through the lab, and there’s too much to include here, but I encourage you to check through the Blog page to find older research posts which provide updates. These and other projects have been successful thanks to hard work and dedication from students and collaborators.

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

The collaborative work we’ve been doing on broccoli sprouts, gut microbes, and Inflammatory Bowel Disease has had plenty to celebrate this year. In addition to defending her master’s thesis, Johanna authored her first first-authored publication: a review on broccoli anti-inflammatories and current research into how gut microbes can help.

We are also continuing our collaborative investigations into the gut microbiome related to Inflammatory Bowel Disease using mouse models, looking at how dietary components can be used by gut microbes to produce anti-inflammatory compounds that can help the host reduce the symptoms of colitis. In December 2020 and January 2021, we (Drs. Yanyan Li and Tao Zhang and I) ran a mouse trial that generated hundreds of samples, and we have been processing them all year! Over the fall in 2021, our collaborators at the University of Vermont (Dr. Gary Mawe, Molly Hurd, Brigitte Lavoie) ran two more small mouse trials to test some exciting new things. We are days away from submitting both of these for review at a scientific journal.

We are also preparing to run a small pilot project in 2023 looking at broccoli sprout diets in humans, as well as follow up with previously isolated bacteria from mice. We’ll need to screen over 800 bacteria for certain enzyme capabilities and usefulness in producing anti-inflammatories. And, we received funding to continue our investigations into how location in the gut, age, and cooking preparation affects the interaction between diet, gut microbes, and host health! Marissa Kinney will be joining #TeamBroccoli as a Master’s of Science student in Microbiology soon, to help us with all these exciting projects.

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The Ishaq Lab has also been very busy working on projects to investigate how, when, and from where Atlantic sea scallops get their microbes.

In 2021, a pilot study got funded to begin collaborative research with a team at UMaine (Drs. Erin Grey, Jen Perry, Tim Bowden) and the Downeast Institute (Dr. Brian Beal). We collected a few hundred samples from scallops and the biofilms growing in hatchery tanks. Over this year, we have been processing the bacterial community sequencing data and hope to submit a manuscript for peer review and publication soon. This fall, we spent several months processing 115 bacterial isolates through >1800 plates and tubes, thanks to a lot of work from students Ayodeji Olaniyi, Sydney Shair, Keagan Rice, and Lacy Mayo who put in hours and hours leading the efforts on this. We are also grateful to Alaa Rabee, Aaron Williams, Lily Robbins, Ash VanNorwick, and Rebecca Kreeger who provided assistance with media making, inoculating, and the large amount of cleanup (we used glass or autoclavable plastic where possible, and sterilized some single-use plastics to be used as training tools for student education). We were also assisted by Bryanna Dube, who is working on creating outreach/education materials based on our results.

Lobster was back on the menu this year as I finished up a data analysis I had been picking away at for two years. This study is available as a preprint (a research article that is currently being peer-reviewed but isn’t finalized yet).

I’ve been collaborating with a few researchers at the Aquaculture Research Institute, where I have an affiliation. This collaborative project on lobster shell disease and warming ocean waters was begun by researchers at the Aquaculture Research Institute: Debbie Bouchard, Heather Hamlin, Jean MacRae, Scarlett Tudor, Sarah Turner, and Grace Lee.

Microbes and Social Equity

The Microbes and Social Equity working group turned 3 years old in December, and is currently at >170 members plus ~100 newsletter subscribers (you can join either list here)! We grew so much that in 2022 that we wrote a separate end of year summary for the group, which will be published soon.

Teaching

This was a busy year for teaching, as I teach 2 courses in the fall and 2 in the spring, which total ~180 students per year. This year, to accommodate disruptions to student schedules over the past few years, I also taught a handful of independent study versions of the Capstone courses for students who could not fit them into their schedule in the recommended semesters. These are considered part of my assigned workload since I taught students who otherwise would have taken this with me during a scheduled course offering, but they did add to my long list of demands for my time this year. There is too much material on my teaching to go into detail here, but I recommend checking out my previous posts on listening to your microbes (a creative assignment), responsible conduct of research (something I integrated into coursework), moving to suggested deadlines, choosing a graduate school, and how departments decide on their curricula.

Website and social media stats

The website gained a phenomenal amount of traffic this year, largely due to MSE, and with just a few days left in the year we clocked nearly 12,500 visitors and nearly 25,000 views!

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

I published a record 82 blog posts, but this included a few dozen that were just promoting events for MSE.

I wrote more than 34,900 words in posts this year!

The page on the 2021 MSE speaker series was the most popular for visitors this year, with MSE symposia and the 2022 series also being popular.

People shared this content on a variety of social media outlets.

Looking ahead to 2023

The Ishaq Lab has several major projects lined up for 2023, including a broccoli sprout diet pilot project with volunteers from the Bangor area, screening >800 bacteria for their ability to produce anti-inflammatories which we isolated from a mouse study using the broccoli sprout diet, investigating how the age of mice alters the effectiveness of the broccoli sprout diet, identifying 150 bacteria isolated from scallop hatchery tanks, and using >700 DNA samples collected from scallop tanks over a 3 month period to investigate what happens to the bacterial communities in tanks during a larvae rearing trial.

This past year, I was busier than I expected to be, in part because pandemic disruptions began to manifest in students needing much more time with advising to sort out their schedules within tight time constraints with fewer course overrings to choose from, and from faculty and staff taking the early retirement incentive from UMaine to reduce budget deficits which shifted their workload to remaining faculty. This is in addition to the ongoing supply shortages and delays that we are all still facing, which causes disruptions to project timelines and makes sorting out annual budgets that much more time consuming. But, I also had a few extra pilot projects or side projects running, which require more effort and communications in the early stages to get things moving.

Collectively, my workload in 2022 far exceeded what I should be taking on, and I had to set firmer limits on requests for my time, turn down opportunities, and catch up on work during my personal time to an excessive degree. In giving a talk to undergraduates in STEM fields, I urged them to build skills in time management, scheduling in advance, learning when they are able to say no (which is less frequent than you would think), and learning how to prioritize activities when they are unable to say no to requests for their time. My advice to them was that if you are forced to work during your personal time, then you should be working on the activities which benefit you the most. This is particularly important in academia where no matter how many hours I work, I can’t earn bonuses or renegotiate my planned salary increases, but yet there is an ever-increasing need for more productivity and effort. Thus, when I have been working overtime I selected activities which benefit me in other ways, and usually takes the form of writing manuscripts (which I enjoy), proposals (a Sisyphean but necessary task), or blog posts.

In support of healthy restraints on my working hours, I will have to continue to limit requests for my time in 2023 to those which build on my existing directions of teaching and research. Unfortunately, this means turning down many potential collaborations in completely new areas of research for me, to facilitate my focus on the wealth of research and teaching I currently have which fill my days (and weekends) with novelty, surprise, and joy.

Happy New Year!!

Catch of the day: lots and lots of microbiology

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Over the past few months, a large team of undergraduate, graduate, and postdoctoral researchers, and I, have been processing hundreds of samples from our scallop hatchery microbiome project. As 2022 winds down, so does the first phase of our lab work, and we are taking a well-deserved break over the holidays before we launch additional lab work, data analysis, and manuscript writing in 2023.

In 2021, the Ishaq Lab, collaborators at UMaine, and collaborators at the Downeast Institute ran a pilot project to investigate the bacteria that associate with sea scallop larvae in hatcheries, and how this is develops in relation to bacteria in hatchery tanks over time. For that project, we collected hundreds of culture plates with a specialized media that selects for certain species of bacteria.

When tanks are drained and cleaned every two days, cotton swabs are rolled across part of the bottom or side of the tank and used to inoculate bacteria onto these culture plates. This is part of a routine screening for pathogens, and don’t worry, we aren’t finding bacteria that causes disease in humans. But, these screening plates creates a useful starting point for our research on bacterial community dynamics.

Tank swab samples are used to inoculate TCBS plates to screen for Vibrio and similar bacteria

We received over 200 of these TCBS culture plates, and from them we isolated 140 bacteria in 2021 and early 2022 which we archived at -80 degrees Celsius. This was part of Sarah Hosler’s master’s of science thesis in August of 2022, and has since been passed to Ayodeji Olaniyi for part of his master’s of science thesis.

This fall, we were able to recover 115 of these isolates from the deep freeze, and tested them on 12 different media in duplicate, which created >1800 cultures plates and tubes, and 230 microscope slides!

This massive undertaking would not have been possible without a large team helping with the lab work, including rockstars Ayodeji Olaniyi, Sydney Shair, Keagan Rice, and Lacy Mayo who put in hours and hours leading the efforts on this. We are also grateful to Alaa Rabee, Aaron Williams, Lily Robbins, Ash VanNorwick, and Rebecca Kreeger who provided assistance with media making, inoculating, and the large amount of cleanup (we used glass or autoclavable plastic where possible, and sterilized some single-use plastics to be used as training tools for student education). We were also assisted by Bryanna Dube, who is working on creating outreach/education materials based on our results.

Now, our team will focus on analyzing the results of all these microbiology tests and look for trends. Some will also be heading to the Perry Lab to learn how to perform quantitative polymerase chain reactions (qPCR), in which we use a modified version of DNA replication to count the copies of specific genes. We will use this to look for genes which confirm the identity of our bacteria.

Beginning in summer 2022, the Ishaq Lab has also been part of a state-wide research and commercial collaboration to understand and improve sea scallop production in hatcheries and farms. As part of that project, we received 1500 DNA samples from different hatchery tanks or larvae over the summer/fall rearing season.

Gloria Adjapong is a Postdoctoral Fellow at the UMaine Cooperative Extension Veterinary Diagnostics Lab, and she has been graciously extracting these samples as part of her cross-training in the Ishaq Lab. We will use the extracted DNA to sequence the bacterial communities to identify which bacteria are present, and when, to understand microbial community dynamics over time and in relation to scallop health.

The Ishaq Lab welcomes a new grad student, Marissa Kinney!

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The Ishaq Lab is pleased to welcome Marissa Kinney as a Master’s of Science student in Microbiology, beginning in January 2023! She’ll be joining ‘Team Broccoli‘ to investigate the 806 bacteria we isolated from the digestive tracts of mice eating a broccoli sprout diet, in a previous experiment on broccoli sprouts, microbes, and resolving colitis.

Marissa is a recent graduate of the UMaine Microbiology bachelor’s program, where she was part of an interdisciplinary research group and was the first author on a scientific publication this year: Suppression of Methicillin-Resistant Staphylococcus aureus and Reduction of Other Bacteria by Black Soldier Fly Larvae Reared on Potato Substrate.

Marissa Kinney

Marissa Kinney 

Master of Science student, Microbiology and Animal and Veterinary Sciences

Blurb: Marissa is a Masters student who loves learning and bench microbiology. She 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. Since 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 feels a big pull towards laboratory work and academic research. She recently joined the Ishaq lab and is excited by the new opportunities this position brings. 

Johanna’s review published on how gut microbes can make anti-inflammatory compounds when you eat broccoli

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A massive literature review led by Johanna Holman, and featuring our collaborative team of broccoli sprout and microbes researchers, was accepted for publication!

As part of her master’s of science thesis, Johanna Holman reviewed hundreds of journal articles on anti-inflammatory, health-promoting dietary compounds in broccoli and other vegetables or fruits, and how microbes in the digestive tract can transform inactive precursors from foods into those beneficial compounds. This is part of a broader research collaboration on how glucoraphanin in broccoli sprouts can be made into sulforaphane, which acts as an anti-inflammatory in humans. Humans are unable to convert glucoraphanin to sulforaphane, and a small amount of this occurs naturally thanks to enzymes in the broccoli sprouts. But, certain gut microbes can make the conversion and this has helped resolve colitis and other symptoms in mice in laboratory trials (manuscripts in preparation).

A diagram with two panels, and a cartoon mouse in the middle. The cartoon mouse is eating broccoli, and a cartoon of the digestive tract is overlaid on the mouse's abdomen. Lines emanating from the broccoli point to the left panel, and show the compound glucoraphanin being converted into sulforaphane by the myrosinase enzyme. Lines emanating from the colon of the mouse point to the panel on the right, showing the same biochemical conversion by gut microbes.
Artwork by Johanna Holman.

If you aren’t familiar with broccoli sprouts, a lovely review on their history, current food culture, and safe production was just published by some of our colleagues: Sprout microbial safety: A reappraisal after a quarter-century.

Check out the review

Holman, J., Hurd, M., Moses, P.,  Mawe, G.,  Zhang, T., Ishaq, S.L., Li, Y. 2022. Interplay of Broccoli/Broccoli Sprout Bioactives with Gut Microbiota in Reducing Inflammation in Inflammatory Bowel Diseases. Journal of Nutritional Biochemistry, in press.

Abstract

Inflammatory Bowel Diseases (IBD) are chronic, reoccurring, and debilitating conditions characterized by inflammation in the gastrointestinal tract, some of which can lead to more systemic complications and can include autoimmune dysfunction, a change in the taxonomic and functional structure of microbial communities in the gut, and complicated burdens in a person’s daily life. Like many diseases based in chronic inflammation, research on IBD has pointed towards a multifactorial origin involving factors of the host’s lifestyle, immune system, associated microbial communities, and environmental conditions. Treatment currently exists only as palliative care, and seeks to disrupt the feedback loop of symptoms by reducing inflammation and allowing as much of a return to homeostasis as possible. Various anti-inflammatory options have been explored, and this review focuses on the use of diet as an alternative means of improving gut health. Specifically, we highlight the connection between the role of sulforaphane from cruciferous vegetables in regulating inflammation and in modifying microbial communities, and to break down the role they play in IBD.

News Center Maine interviews Yanyan and Sue about broccoli sprouts!

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Yanyan Li and I sat down yesterday with Carly D’Eon, a reporter with News Center Maine, to talk about our ongoing research into broccoli sprouts, gut microbes, and Inflammatory Bowel Disease!

The story and the video can be found here.

Lobster shell microbes, epizootic shell disease, and climate change preprint manuscript is now online

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A cookie in the shape of a lobster with icing to make it look like a pirate.

It’s been a few years in the making, but our draft manuscript on lobster shell microbes, epizootic shell disease, and climate change is available online as a preprint (not yet peer reviewed)! You can read the preprint here, and the summary is below.

I joined this project back in the summer of 2020, when I was given a large 16S rRNA gene sequence dataset of bacterial communities from the shells of lobsters by a research group at UMaine who had been studying lobster health for some time. My first point of contact on the project was Jean MacRae, an Associate Professor of Civil and Environmental Engineering at UMaine, who had been working on bacterial community sequencing on other projects which I’ve been involved in, and who has been involved with MSE, and this will be our fourth publication together!

Jean introduced me to the original research team, including Debbie Bouchard, who is the Director of the Aquaculture Research Institute and was researching epizootic shell disease in lobsters for her PhD dissertation; Heather Hamlin, Professor and Director of the School of Marine Sciences; Scarlett Tudor, the Education and Outreach Coordinator at the ARI; and Sarah Turner, Scientific Research Specialist at ARI.

I used the data as a training opportunity for Grace Lee, who at the time was an undergraduate at Bowdoin College participating in the abruptly cancelled summer Research Experience for Undergrads program at UMaine in summer 2020. Instead, Grace joined my lab as a remote research assistant and we worked through the data analysis over the summer and fall. Grace has since graduated with her Bachelor’s of Science in Neuroscience, obtained a Master’s of Science at Bowdoin, and is currently a researcher at Boston Children’s Hospital while she is applying to medical school.

Earlier this year, the research team, along with social science Masters student Joelle Kilchenmann, published a perspective/hypothesis piece which explored unanswered questions about how the movement of microbes, lobsters, and climate could affect the spread of epizootic shell disease in lobsters off the coast of Maine.

A steamed lobster on a plate.

“Warmer water temperature and epizootic shell disease reduces diversity but increases cultivability of bacteria on the shells of American Lobster (Homarus americanus).”

Suzanne L. Ishaq1,2,, Sarah M. Turner2,3, Grace Lee4,5,M. Scarlett Tudor2,3, Jean D. MacRae6, Heather Hamlin2,7, Deborah Bouchard2,3

  • 1 School of Food and Agriculture; University of Maine; Orono, Maine, 04469; USA.
  • 2 Aquaculture Research Institute; University of Maine; Orono, Maine, 04469; USA.
  • 3 Cooperative Extension; University of Maine; Orono, Maine, 04469; USA.
  • 4 Department of Neuroscience, Bowdoin College, Brunswick, ME 04011; USA.
  • 5 Boston Children’s Hospital, Boston, MA 02115; USA.
  • 6 Department of Civil and Environmental Engineering; University of Maine; Orono, Maine, 04469; USA.
  • 7 School of Marine Sciences; University of Maine; Orono, Maine, 04469; USA.

Summary

The American lobster, Homarus americanus, is an economically valuable and ecologically important crustacean along the North Atlantic coast of North America. Populations in southern locations have declined in recent decades due to increasing ocean temperatures and disease, and these circumstances are progressing northward. We monitored 57 adult female lobsters, healthy and shell-diseased, under three seasonal temperature cycles for a year, to track shell bacterial communities using culturing and 16S rRNA gene sequencing, progression of ESD using visual assessment, and antimicrobial activity of hemolymph. The richness of bacterial taxa present, evenness of abundance, and community similarity between lobsters was affected by water temperature at the time of sampling, water temperature over time based on seasonal temperature regimes, shell disease severity, and molt stage. Several bacteria were prevalent on healthy lobster shells but missing or less abundant on diseased shells, although putative pathogens were found on all shells regardless of health status.

Collaborative paper published on winter wheat, farming practices, and climate!

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The second paper from Tindall’s master’s work at Montana State University in the Menalled Lab has been accepted for publication! Tindall defended her master’s in August 2021, and has been working at a plant production company in Bozeman since then.

Ouverson, T., Boss, D., Eberly, J., Seipel, T.,  Menalled, F.D., Ishaq, S.L. 2022. Soil  bacterial community response to cover crops, cover crop termination, and predicted climate conditions in a dryland cropping system. Frontiers in Sustainable Food Systems.

Abstract

Soil microbial communities are integral to highly complex soil environments, responding to changes in aboveground plant biodiversity, influencing physical soil structure, driving nutrient cycling, and promoting both plant growth and disease suppression. Cover crops can improve soil health, but little is known about their effects on soil microbial community composition in semiarid cropping systems, which are rapidly becoming warmer and drier due to climate change. This study focused on a wheat-cover crop rotation near Havre, Montana that tested two cover crop mixtures (five species planted early season and seven species planted mid-season) with three different termination methods (chemical, grazed, or hayed and baled) against a fallow control under ambient or induced warmer/drier conditions. Soil samples from the 2018 and 2019 cover crop/fallow phases were collected for bacterial community 16S rRNA gene sequencing. The presence and composition of cover crops affected evenness and community composition. Bacterial communities in the 2018 ambient mid-season cover crops, warmer/drier mid-season cover crops, and ambient early season cover crops had greater richness and diversity than those in the warmer/drier early season cover crops. Soil microbial communities from mid-season cover crops were distinct from the early season cover crops and fallow. No treatments affected bacterial alpha or beta diversity in 2019, which could be attributed to high rainfall. Results indicate that cover crop mixtures including species tolerant to warmer and drier conditions can foster diverse soil bacterial communities compared to fallow soils.

Figure 1, showing a schematic of the fields and experimental design.

Related works from that research group include:

Li and Ishaq labs receive NIH R15 award to study broccoli bioactives, gut microbes, and inflammation!

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The Li and Ishaq labs at UMaine, along with collaborators from multiple institutions, have been awarded R15 funding from the National Institute Of Diabetes And Digestive And Kidney Diseases of the National Institutes of Health!

This award will complement other projects/awards led by our team, which has been investigating inflammatory bowel diseases, anti-inflammatories, gut microbes, and nutrition, separately for decades and collaboratively for over two years.

  • Dr. Yanyan Li, PhD (lead PI), Assistant Professor at the University of Maine with expertise in nutrition and food science, particularly dietary bioactives and colitis;
  • myself (co-PI), with expertise in host-associated microbiology, especially GI tract;
  • Dr. Grace Chen, MD, PhD (co-I), Associate Professor at the University of Michigan, expertise in mouse models for gut microbiome and colonic host immune responses;
  • Dr. Tao Zhang, PhD (consultant), Assistant professor at Binghamton University, with expertise in metabolism, kinetics, and bioanalysis of natural products;
  • Dr. Gary Mawe, PhD (consultant), Professor at the University of Vermont, with expertise in translational research on GI tract regulation, inflammation, and IBD;
  • Dr. Peter Moses, MD (consultant), Professor Emeritus at the University of Vermont College of Medicine and Senior Researcher at GSK, with expertise in IBD and functional gastrointestinal disorders.

R15 Research Enhancement Awards are designated for projects which involve a large number of student researchers. Between the Li and Ishaq labs, there are three current graduate students, and two former undergrads who have contributed to this research, and we anticipate bringing in 1-2 additional graduate students and almost a dozen undergrads in the next year! That will include undergrads in Honors, Top Scholars, and Capstone programs at UMaine. We’ve also been assisted by the work of students, postdocs, technicians, and investigators through our collaborators, and we are ecstatic about the opportunity to continue to grow our team across institutions. And, this project will generate research that will feed back into education at UMaine through the courses that we teach, such as my microbiomes and DNA sequence analysis courses.

“Harnessing gut microbiota to reduce inflammation using broccoli-sprout diets.”

Project Summary:

Inflammatory bowel disease (IBD) is a poorly understood gastrointestinal (GI) condition characterized by inflammation. The prevailing theory is that combined genetic and environmental factors disrupt the host immune system’s interaction with gut microbiota. Our central hypothesis is that consumption of specific broccoli sprout preparations elicits changes in the gut microbiota that not only improve the production of anti-inflammatory bioactives, but also promote intestinal homeostasis. Our labs have shown there is an anatomical pattern along the GI tract where broccoli sprout-derived bioactive levels are high which correspond to diet-induced changes in gut microbial communities. We showed that gut microbiota contribute to the transformation of inactive precursors to bioactives, and that specific broccoli sprout preparations alter their capacity for biotransformation, and the susceptibility of mice to colitis. However, a significant knowledge gap remains regarding the mechanisms by which dietary bioactives modify disease risk and the role of gut microbiota. Our immediate goal is to identify the mechanisms by which broccoli sprout diets affect susceptibility to IBD in mice. Our long-term goal is to develop a dietary preparation of
broccoli sprouts which has therapeutic effects against IBD in humans. Our innovative approach uses different preparations of broccoli sprouts to help differentiate gut microbiota versus plant-derived
enzymatic activities. We employ a combination of “omics” approaches to spatially-map the microbial community and metabolite profile changes along the GI tract, to better assess changes induced by broccoli sprout diets. We complement “omics” approaches with culturing, and validate our study design using two complementary models for strategic research.

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

Aim 1 tests the hypothesis of an anatomical pattern where the GI tract microbiota transform broccoli compounds into bioactives, and helps us determine whether this microbial biotransformation is sensitive to dose of broccoli compounds. We will use our established DSS-mouse-model of ulcerative colitis to investigate the effects of different broccoli sprout preparations and concentrations on the microbiota along the GI tract; on the resulting concentration of bioactives in gut tissues; and on the development of colitis in mice.

A cartoon schematic of the experimental design of the project. Four mice are at the top, two have "DSS" written above them, one of which is also holding a broccoli sprout. One of the mice without DSS written on it is holding a broccoli sprout. Below the mice is a cartoon of the digestive tract with arrows emanating from it to indicate samples of microbes will be taken from different locations. The microbe images have arrows pointing to culturing equipment, and also to a biochemical pathway showing the compound glucoraphanin being converted to sulforaphane.
Created by Sue Ishaq, made with Biorender

Aim 2 tests the benefits of using an immunosuppressed mouse model in the dietary prevention study to provide a stronger translational strategy for the use of broccoli sprouts for IBD prevention. When exposed to a specific bacterial pathogen, the immunosuppressed mice develop chronic enterocolitis resembling Crohn’s disease. This diet-based approach provides critical information for developing accessible and equitable strategies for improving health of IBD patients.

A cartoon schematic of the experimental design of the project. Two mice are at the top, with the label "IL-10" crossed out above them. One mouse is also holding a broccoli sprout. Below the mice is a cartoon of the digestive tract with arrows emanating from it to indicate samples of microbes and tissue will be taken from different locations. The words weight and plasma indicate those will also be collected. The plasma and tissue samples will be used for mass-spectroscopy and histology, and the microbes will be used for DNA sequencing.
Created by Sue Ishaq, made with Biorender

Li and Ishaq labs receive Allen Foundation funding to research broccoli bioactives!

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The Allen Foundation awarded Dr. Yanyan Li, Assistant Professor of Food Science and Human Nutrition, and myself funding for a pilot project in people on broccoli sprouts, the gut microbiome, anti inflammatory compounds, and health! Dr. Li and I, as well as a team of other researchers, have been collaborating over the last three years to understand how certain gut microbes create an anti-inflammatory compound using a compound in broccoli sprouts, and how we can use this action to calm colitis. Over the next 18 months, we will be recruiting a small group of people to participate in a diet trial. This will form the first part of the PhD work for Johanna Holman, who recently defended her master’s of science at UMaine.

Project Summary:

There is increasing evidence that diet and the gut microbiota have significant impact on human health and thus impact susceptibility to disease such as inflammatory bowel disease. Indeed, a Westernized diet has been associated with higher risk for developing inflammatory bowel disease, primarily as ulcerative colitis and Crohn’s disease, while a diet rich in fruits and vegetables tends to reduce risk. Our preliminary data suggests that a specific whole-food preparation of broccoli sprouts protects against the development of colitis in a chemically-induced mouse model as well as in a transgenic mouse model of Crohn’s disease. Furthermore, the gut microbiome contributes to the generation of the active anti-inflammatory component, sulforaphane, from broccoli sprouts, and the microbiome, in turn, is altered by exposure to broccoli sprouts or its metabolites. Thus, our long-term goal is to understand the interactions between anti-inflammatory bioactives of broccoli sprouts and the gut microbiome. The current proposal aims to increase our understanding of the nutrigenomics of the human microbiome and a broccoli sprout diet in healthy subjects. Our goal is to determine the feasibility of incorporating a specific broccoli sprout preparation into whole-food diets to increase levels of anti-inflammatory bioactives from broccoli sprouts in healthy humans. These directly address the foundation’s priority of “bringing the promise of nutrigenomics or nutritional genomics to realization”. Results from this study will help determine the feasibility and potential efficacy of a whole food approach in promoting intestinal homeostasis and mitigating risk of developing inflammatory bowel disease.

Diagram of the chemical conversion of glucoraphanin to sulforaphane. In panel A, the process is shown using the plant enzyme myrosinase, and in panel B, the process is shown using bacterial myrosinase-like enzymes. In the middle of the diagram, there is a cartoon mouse eating broccoli. Panel A points to the broccoli, where that action occurs, and panel B points to the gut, where microbial conversion occurs,
Figure from Holman et . in review, artwork by Johanna Holman. Glucoraphanin hydrolysis. A. GLR hydrolysis in the presence of myrosinase upon damage to the broccoli plant. Epithiospecifier protein preferentially converts GLR to SFN-nitrile. B. GLR hydrolysis has been demonstrated by gut bacteria in the colon of mammals.  Low pH environments favor conversion to SFN-nitrile.

Alexis wraps up her REU project!

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Last week, undergraduate Alexis Kirkendall concluded her 10-week Research Experience for Undergraduates (REU) program at the University of Maine. Over that time, she has been an integral member of the Ishaq lab, and had assisted with lab work for multiple projects, comparing microscopy staining protocols, training students, assisting with laboratory management and safety regulation checks, and more. She picked up skills in animal sample collection, microscopy and staining, parasitology, culture media preparation, DNA extraction, and data visualization in R. Alexis also helped create some of the marketing materials for the Microbes and Social Equity Symposium in July, and facilitated group discussions as a note taker.

At the end of the program, REU students create posters and short presentations of their efforts over the summer. The presentations were last week, but you can check out the poster below.

Alexis is heading back to Ohio for her next year at Heidelberg College where, in addition to studying science, she is leading initiatives to make the campus more accessible and inclusive. But, we hope to see her back in Maine sometime in the future!

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