Adwoa defended her doctoral dissertation!!

Congratulations to Dr. Adwoa Dankwa, who defended her doctoral dissertation today on the microbial communities and metabolites in kombucha and kefir!

Adwoa has a background in plant pathology, but she has been working with her adviser, Dr. Jennifer Perry, in the Human Nutrition and Food Sciences program for the last few years on understanding the microbial and chemical composition of fermented non-dairy low alcohol beverages and how these influence consumer acceptability over time.

I’ve been mentoring Adwoa on microbial community data analysis for her project, and look forward to the manuscripts in development from her work. She and I previously published together when she completed the data analysis for a project in my DNA sequencing data analysis class.

Adwoa is beginning a postdoctoral research position in the Perry, and we are all delighted that she’ll continue to be here to brighten our days.

Adwoa originally hails from Ghana, and she generously gave the committee some gifts which were etched with kinds words and symbols from home.

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

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.


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!

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

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.


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.

Li and Ishaq labs made the UMaine News!

UMaine News recently highlighted some of the collaborative work that Yanyan Li and I have been doing at UMaine! You can read more about our projects here, here, and here.

This work features researchers from other universities, including:

•Dr. Tao Zhang, PI, SUNY Binghamton

•Dr. Grace Chen, PI, MSU

•Dr. Gary Mawe, PI, UVM

•Molly Hurd, PhD student, UVM

•Bridgette Lavoie, RA, UVM

•Dr. Peter Moses, PI, Finch Therapeutics

•Johanna Holman, MS student, Umaine

•Lola Holcomb, PhD student, UMaine

•Louisa Colucci, undergrad at the time, Husson

Joe Balkan, Undergrad, Tufts

•Dr. Emma Perry, UMaine Microscopy Facility

In addition to the two new funding sources listed in the article, we have been supported by:

•Maine Agricultural and Forestry  Experimental Station

•ME0-22102 (Ishaq) and ME0-22303 (Li)

•USDA-NIFA-AFRI Foundational Program [Grant No. 2018-67017-27520]

•UMaine Institute of Medicine

•Maine Center for Genetics in the Environment

• UMaine GSBSE

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

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.


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!

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!

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!

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!

Sarah defends her master’s thesis defense!

Sarah Hosler passed her Master’s of Science these defense (we knew she would succeed)!! Sarah has worked incredibly hard over the last two years to broaden her research skills and conduct four completely different pilot projects. Her defense presentation focused on the two main projects, but was a wonderful way to see that progression all at once and to reflect on her growth as a lab manager and researcher. She has also earned the designation of “second Ishaq Lab grad student to defend”.

The defense was attended by her thesis committee, students in the Ishaq lab, collaborators on this project, friends and family, and Izzy the dog (pictured, and yes, Sarah preferred this picture of her at her defense to a portrait of herself. Sarah will officially pass after a few revisions to her thesis and a formal acceptance by the committee members, which is standard for graduate defenses.

After wrapping up a few things in Maine, Sarah will be heading to Pennsylvania to take a position as Student Program Coordinator for middle and high school aged students at Albright College, where she obtained her Bachelor’s of Science. Congrats on the defense and on the next stage of your career!

“Weaving An Interdisciplinary Microbiome Career Using Threads From Different Ecosystems”.