We’re thrilled to share that Dr. Lola Holcomb, who recently completed her PhD in Biomedical Science at the University of Maine, will be joining Dr. Eben Estell’s lab at the University of New England as a Postdoctoral Research Fellow! Dr. Estell is a new faculty member starting up a lab developing tissue engineered models for bone mechanobiology, and this position will focus on data analysis and conceptual models on how cells interact with mechanical structures, to create better medical treatments.
During her doctoral work in the Ishaq Lab, Lola investigated how diet and gut microbiota interact to influence host health, with a particular focus on glucosinolate-metabolizing bacteria and the effects of broccoli sprout consumption. Her research combined bioinformatics, metagenomic data analysis, and microbial ecology, resulting in new insights into how diet-driven changes in microbial function relate to host physiology.
In her postdoctoral position, Lola will be bridging her bioinformatics expertise with her original background in exercise physiology to explore how mechanical loading, irisin, and bone cell biology are interconnected. This new role beautifully integrates her computational skills with her passion for physiology and health — a truly interdisciplinary continuation of her scientific journey.
One of Lola’s favorite memories from her time in the lab was traveling together to the ISME conference in Cape Town, where she presented her work to an international audience of microbial ecology researchers. It was a fantastic milestone that captured her growth as both a scientist and communicator.
We can’t wait to see where Lola’s research takes her next! Luckily, Lola will still be collaborating a bit with the Ishaq Lab to finish out several projects from her doctoral work. This includes genomic comparisons of bacteria which can convert glucoraphanin into sulforaphane, metagenomics of the gut bacteria of people consuming broccoli sprouts every day for a month, and several collaborations on human microbiome research.
Bioinformatics rockstar, Lola Holcomb, successfully defended her PhD dissertation today on “Anti-Inflammatory Interactions between Gut Microbiota and Broccoli Sprouts”!!!!
Holcomb, Lola. “Anti-Inflammatory Interactions between Gut Microbiota and Broccoli Sprouts”. (2025). University of Maine. Doctor of Philosophy Dissertation (forthcoming). Presentation.
Lola’s contributions to and leadership in the Ishaq Lab Team have led to numerous publications, presentations, and immeasurable professional growth and camaraderie within the group. Her contributions to our research helped us open a new avenue of focus, sparked the imagination of several undergraduates who are now involved in research, and improved the mood and collegiality of the research group with her humor, insightfulness, and poignant questions. Lola has been more of a colleague than a trainee, and the lab is delighted to see how much she’s grown as a researcher. Lola is currently searching for positions as a postdoctoral researcher, bioinformatician, or Assistant Professor at an undergraduate-focused university or college. She’ll continue to collaborate with the Ishaq Lab, as we have multiple manuscripts in review or in preparation for peer review on which she is an author.
Lola entered as a rotating first-year student in March 2022 in the Graduate School of Biomedical Sciences and Engineering program, and declared the Ishaq Lab her dissertation lab soon after, and starting in fall of 2022 was accepted into the NRT funded for One Health in the Environment program. 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 performed 16S data analysis for multiple lab projects and developed 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 instructed a graduate-level Genetics course, assisted in Dr. Ishaq’s 16S DNA Sequence Data Analysis course, tutored several Biology undergraduate students, and served as a GSBSE senator in the Graduate Student Government here at UMaine.
Some of the lab are lucky enough to be able to travel to Cape Town, South Africa this August for the 19th International Symposium on Microbial Ecology (ISME)!!! This conference is held in different host cities, and brings together microbiologists from around the world to celebrate our work and foster our scientific community.
Session: Integrating equity into microbiome science from crops to communities
Convenors Sue Ishaq, University of Maine, USA Adolphe Zeze, Institut National Polytechnique Félix Houphouët-Boigny, Côte d’Ivoire
Date: 20-Aug-2024, session from 11:00 to 13:00. Location: Meeting Room 2.6 (2.61 – 2.64) of CTICC1 in Cape Town.
About the session: Microorganisms are critical to many aspects of biological life, and the collective microbial community, or microbiome, can be impacted by environmental factors which may be driven by social, economic, medical, or political constraints that restrict available choices and may impact our health. This session explores the way that microbes connect to social disparities, and how microbial ecology can be used to benefit public health and vulnerable populations.
Photo credit Johanna Holman.
Characterizing Gut Bacteria Associated with Sulforaphane Production
Date: 19-Aug-2024, live session from 16:30 to 17:30. Poster number: PS1.02.050. Section: Understanding microbiome dynamics to improve human health
Affiliations: 1 Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA; 2 School of Food and Agriculture, University of Maine, Orono, Maine, USA; 2 Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA; 3School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA.
Abstract: Broccoli sprouts contain glucosinolates which can be converted into sulforaphane, an anti-inflammatory compound. Mammals do not produce the essential digestive enzymes to perform this conversion, fortunately, somegut bacteria do, and this results in high sulforaphane in the colon and systemically. Sulforaphane production has implications in treating inflammatory bowel diseases such as ulcerative colitis. Bacterial samples were collected from 40 all-male SPFC57BL/6 mice. Divided into four groups, mice received a combination, or lack thereof, of 2.5%dextran sodium sulfate in drinking water to induce ulcerative colitis and/or steamed broccoli sprouts at 10% of the diet. Following the trial, bacteria were isolated from jejunum and colon digesta- and mucosal-associated contents. Bacteria were grown on bacto-tryptone yeast broth media in anaerobic conditions. Collected bacteria were analyzed based on morphological data. Following initial culturing bacteria were placed in 96-well plates amongst bacto-tryptone yeast broth in four groups: with glucose, without glucose, with glucoraphanin, and with sinigrin. Plates were incubated anaerobically for 24 hours followed by growth being measured via spectrophotometry, to assess potential as a probiotic. Over four hundred bacteria were assessed, multiple of which showed signs of glucosinolate conversion. Across gram stains, approximately 80% of all analyzed showed to be gram +.
Graphic Designed by Indigo Millisor.
Funding Sources: This work was funded by the NIH, Crohn’s and Colitis Foundation, and NSF NRT.
Steamed broccoli sprouts alleviate gut inflammation and retain gut microbiota against DSS-induced dysbiosis.
Johanna M. Holman1, Lola Holcomb2, Louisa Colucci3, Dorien Baudewyns4, Joe Balkan5, Grace Chen6, Peter L. Moses7,8, Gary M. Mawe7, Tao Zhang9, Yanyan Li1*, Suzanne L. Ishaq1*
Date: 19-Aug-2024, live session from 10:00 to 11:00 Poster number: PS1.02.007 Section: Understanding microbiome dynamics to improve human health
Affiliations: 1 School of Food and Agriculture, University of Maine, Orono, Maine, USA; 2 Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA; 3 Department of Biology, Husson University, Bangor, Maine, USA; 4 Department of Psychology, University of Maine, Orono, USA; 5 Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA; 6 Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA; 7 Departments of Neurological Sciences and of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA: 8 Finch Therapeutics, Somerville, Massachusetts, USA; 9 School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA.
Abstract: Inflammatory bowel diseases are devastating conditions of the gastrointestinal tract with limited treatments, and dietary intervention may be effective, affordable, and safe for managing symptoms. Research has identified inactive compounds in broccoli sprouts that may be metabolized by the gut microbiota into key anti-inflammatories. Our research set out to identify biogeographic locations of participating microbiota and correlate that to health outcomes. We fed specific pathogen free C57BL/6 mice either a control diet or a 10% steamed broccoli sprout diet, and gave a three-cycle regimen of 2.5% dextran sulfate sodium in drinking water over 40 days to simulate ulcerative colitis. We monitored body weight, fecal characteristics and lipocalin, and sequenced bacterial communities from the contents and mucosa of the jejunum, cecum, and colon. Mice fed the broccoli sprout diet while receiving dextran sulfate sodium performed better than mice fed control diet for all disease parameters, including increased weight gain (2-way ANOVA, p < 0.05), lower Disease Activity Index scores (2-way ANOVA, p < 0.001), and higher bacterial richness (linear regression model, p < 0.01). Bacterial communities were assorted by gut location except in the mice receiving the control diet and colitis-inducing treatment (Beta-diversity, ANOVA, p < 0.05). Importantly, our results suggest that broccoli sprouts abrogated the effects of dextran sulfate sodium on the gut microbiota, that colitis erases biogeographical patterns of bacterial communities, and that the cecum is not likely to be a contributor to colonic bacteria of interest, in a mouse model of ulcerative colitis.
Funding Sources: This work was funded by the NIH, USDA, NSF NRT, and UMaine GSBSE.
Consuming steamed broccoli sprouts as part of their diet protected the gut biogeography of microbes — which bacteria was found in which organ sampled– in the intestines of mice who were experiencing chemically induced colitis. Image by Johanna Holman.
Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease.
Lola Holcomb1, Johanna Holman2, Molly Hurd3, Brigitte Lavoie3, Louisa Colucci4, Gary M. Mawe3,Peter L. Moses3,5, Emma Perry6, Allesandra Stratigakis7, Tao Zhang7, Grace Chen8, Suzanne L. Ishaq1*, Yanyan Li7*
Date: 19-Aug-2024, live session from 16:30 to 17:30 Poster number: PS1.02.002 Section: Understanding microbiome dynamics to improve human health
1 Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine 2 School of Food and Agriculture, University of Maine, Orono, Maine 3 Larner College of Medicine, University of Vermont, Burlington, Vermont 4 Department of Biology, Husson University, Bangor, Maine, 5 Finch Therapeutics, Somerville, Massachusetts, 6 Electron Microscopy Laboratory, University of Maine, Orono, Maine 7 School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, 8 Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
Inflammatory Bowel Diseases (IBD) are chronic conditions characterized by inflammation of the gastrointestinal (GI) tract that burden daily life, result in complications, and disrupt the gut microbiome. Many studies on diet and IBD in mice use an ulcerative colitis model, despite the availability of an immune-modulated Crohn’s Disease model. The objective of this study was to establish IL-10 deficient mice as a model for studying the role of dietary broccoli and broccoli bioactives in reducing inflammation, modifying the immune response, and supporting GI tract microbial systems. Interleukin-10-knockout (IL-10-ko) mice on a C57BL/6 background, beginning at age 4 or 7 weeks, were fed either a control diet or one containing 10% raw broccoli sprouts. Diets began 7 days prior to inoculation with Helicobacter hepaticus, which triggers Crohn’s-like symptoms in these immune-impaired mice, and ran for 2 additional weeks. Broccoli sprouts decreased (p < 0.05), fecal lipocalin (LCN2), a biomarker for intestinal inflammation, and fecal blood, diarrhea, and overall Disease Activity Index. Sprouts increased gut microbiota richness, especially in younger mice (p < 0.004), and recruited different communities in the gut (B-diversity, ANOVA, p < 0.001), especially in the colon (B-diversity, ANOVA, p = 0.03). The control group had greater prevalence and abundance of otherwise commensal bacteria which trigger inflammation in the IL-10-ko mice. Helicobacter was within the top-5 most prevalent core genera for the control group, but was not within the top-5 for the broccoli group. Disease parameters and microbiota changes were more significant in younger mice receiving broccoli. A diet containing 10% raw broccoli sprouts may be protective against negative disease characteristics of Helicobacter-induced enterocolitis in IL-10-ko mice, and younger age is the most significant factor (relative to diet and anatomical location) in driving gut bacterial community richness and similarity. The broccoli diet contributes to prevalence and abundance of bacterial genera that potentially metabolize dietary compounds to anti-inflammatory metabolites in the gut, are bacteriostatic against pathogens, and may ease disease severity.
Funding Sources: This work was funded by the NIH, USDA, NSF NRT, and UMaine GSBSE.
The complete author list, Abstract, and Ackowledgements/Funders portions of the paper can be found at the end of this post. This paper is part of a larger Broccoli project, in which we are evaluating the use of broccoli sprouts in the diet to enlist gut microbes to produce anti-inflammatories as a way to resolve symptoms of Inflammatory Bowel Disease.
The Premise
Broccoli sprouts are very high in a compound called glucoraphanin, which is in-active for humans. When glucoraphanin comes in contact with the myrosinase enzyme, also found in the sprouts, it is transformed into sulforaphane, which drives away insect pests but acts as an anti-inflammatory in people!
If you eat raw sprouts, most of this conversion happens when you cut or chew the sprouts, and that anti-inflammatory will get absorbed in your stomach. If you steam or cook the sprouts, you can inactivate the enzyme and leave the glucoraphanin compound alone. Some of your gut microbes are able to use glucoraphanin, and produce the anti-inflammatory sulforaphane right in your gut! We are trying to understand how and when this works, so we can use it to reduce symptoms of Inflammatory Bowel Disease.
The mice in this trial are used to mimic Crohn’s Disease, which is one of the main ways that Inflammatory Bowel Diseases may be classified. Crohn’s Disease is complictaed, and involves an over-active immune response to gut microbes. This is replicated in mice that are bred to lack the genes in the DNA to make interleukin-10 (IL-10). IL-10 is an immune factor that can be used to calm the immune system and tolerate microbes which are not causing harm. Without IL-10, these mice over-react to the presence of bacteria, even those which are not causing harm, and this creates symptoms similar to Crohn’s in people.
We used two age groups of mice, and in each group, half ate a mouse chow (control) diet and half ate the mouse chow with 10% of the chow replaced by raw broccoli sprouts. Crohn’s often develops in childhood and adolescence, so our two age groups of mice reflect the juvenile stage (4-5 weeks old) and the adolescence stage (5-6 weeks old) of symptom onset. After wo weeks of symptoms, we sacrificed the mice and collected as much information as we could.
The Team
The mice, their care during the experiment, and sample collection for this project was graciously provided by University of Vermont researchers Gary Mawe and Brigitte Lavoie, and then-grad-student-now-medical-student Molly Hurd, in 2021. The SUNY Bingamton team, Tao Zhang and Allesandra Stratigakis, processed metabolite and cytokine samples and analyzed those data. The UMaine team (pictured below and led by Sue Ishaq and Yanyan Li) processed and analyzed data from different locations of gut tissue for histolgy and sequencing of bacterial communities, as well as analyzing those data, and took the lead on writing the paper.
The Health Benefits were most obvious in the younger mice
The mice that were eating the broccoli sprouts in their chow and did much better than the control group who ate only mouse chow when symptoms of Crohn’s Disease were induced — and we found something really interesting… The diet worked really well in the younger mice and reduced their symtpoms of inflammation and illness for almost every metric we studied. The older, adolecent mice got some benefit from eating the raw broccoli sprouts, but not nearly as much as the younger mice! Those graphs are shown in the paper.
The Gut Microbes were most changed in the younger mice
Bacterial richness (the number of different types of bacteria present) was increased, but only in younger mice consuming a 10% raw sprout diet, which is useful because pediatric Crohn’s patients usually have fewer types of bacteria present in their gut.
Younger mice consuming broccoli sprouts also had more types of bacteria that are known to convert glucoraphanin into sulforophane, and they had more of the genes needed to do it. Crohn’s patients usually have fewer of these types of bacteria, which are also known to provide other health benefits.
The Next Steps
We are currently working on replicating and expanding this project to include more age groups, so we can understand how different diet preparations of broccoli sprouts impact immune systems and gut microbiota at different developmental periods of life. We are also really interested in understanding how sex in mice, and gender in humans, plays a role in how immune systems and microbial communities develop during a critical phase of life. We have some initial data to suggest that male and female mice respond to different diets and at differnt ages, but we aren’t sure why yet.
We hope to expand our work with people to study how these diets work in the real world, and how we can tailor diet and cooking preparations of sprouts to best meet the needs of people of different ages, health statuses, and tastes.
Lola Holcomb1$, Johanna M. Holman2$, Molly Hurd3, Brigitte Lavoie3, Louisa Colucci4, Benjamin Hunt5, Timothy Hunt5, Marissa Kinney2, Jahnavi Pathak1, Gary M. Mawe3,Peter L. Moses3,6, Emma Perry7, Allesandra Stratigakis8, Tao Zhang8, Grace Chen9, Suzanne L. Ishaq1*, Yanyan Li1*
1 Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469. 2 School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469. 3 Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401. 4 Department of Biology, Husson University, Bangor, Maine, USA 04401. 5 Department of Biology, University of Maine, Orono, Maine, USA 04469. 6 Finch Therapeutics, Somerville, Massachusetts, USA 02143. 7 Electron Microscopy Laboratory, University of Maine, Orono, Maine, USA 04469. 8 School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790. 9 Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA 48109
Crohn’s Disease (CD) is a presentation of Inflammatory Bowel Disease (IBD) that manifests in childhood and adolescence, and involves chronic and severe enterocolitis, immune and gut microbial dysregulation, and other complications. Diet and gut-microbiota-produced metabolites are sources of anti-inflammatories which could ameliorate symptoms. However, questions remain on how IBD influences biogeographic patterns of microbial location and function in the gut, how early life transitional gut communities are affected by IBD and diet interventions, and how disruption to biogeography alters disease mediation by diet components or microbial metabolites. Many studies on diet and IBD use a chemically induced ulcerative colitis model, despite the availability of an immune-modulated CD model. Interleukin-10-knockout (IL-10-KO) mice on a C57BL/6 background, beginning at age 4 or 7 weeks, were fed a control diet or one containing 10% (w/w) raw broccoli sprouts, which was high in the sprout-sourced anti-inflammatory sulforaphane. Diets began 7 days prior to, and for 2 weeks after inoculation with Helicobacter hepaticus, which triggers Crohn’s-like symptoms in these immune-impaired mice. The broccoli sprout diet increased sulforaphane in plasma; decreased weight stagnation, fecal blood, and diarrhea associated; and increased microbiota richness in the gut, especially in younger mice. Sprout diets resulted in some anatomically specific bacteria in younger mice, and reduced the prevalence and abundance of pathobiont bacteria which trigger inflammation in the IL-10-KO mouse, e.g., Escherichia coli and Helicobacter. Overall, the IL-10-KO mouse model is responsive to a raw broccoli sprout diet and represents an opportunity for more diet-host-microbiome research.
Importance
To our knowledge, IL-10-KO mice have not previously been used to investigate the interactions of host, microbiota, and broccoli, broccoli sprouts, or broccoli bioactives in resolving symptoms of CD. We showed that a diet containing 10% raw broccoli sprouts increased the plasma concentration of the anti-inflammatory compound sulforaphane, and protected mice to varying degrees against disease symptoms, including weight loss or stagnation, fecal blood, and diarrhea. Younger mice responded more strongly to the diet, further reducing symptoms, as well as increased gut bacterial richness, increased bacterial community similarity to each other, and more location-specific communities than older mice on the diet intervention. Crohn’s Disease disrupts the lives of patients, and requires people to alter dietary and lifestyle habits to manage symptoms. The current medical treatment is expensive with significant side effects, and a dietary intervention represents an affordable, accessible, and simple strategy to reduce the burden of symptoms.
Acknowledgements: This project was supported by the USDA National Institute of Food and Agriculture through the Maine Agricultural & Forest Experiment Station: Hatch Project Numbers ME022102 and ME022329 (Ishaq) and ME022303 (Li); the USDA-NIFA-AFRI Foundational Program [Li and Chen; USDA/NIFA 2018-67017-27520/2018-67017-36797]; and the National Institute of Health [Li and Ishaq; NIH/NIDDK 1R15DK133826-01] which supported Marissa Kinney, Timothy Hunt, and Benjamin Hunt. Johanna Holman was supported by ME0-22303 (Li), and Lola Holcomb was supported by US National Science Foundation One Health and the Environment (OG&E): Convergence of Social and Biological Sciences NRT program grant DGE-1922560, and the UMaine Graduate School of Biomedical Science and Engineering.
Congratulations to Lola Holcomb, for passing the graduate comprehensive exam!! She now goes from being a PhD student to a PhD candidate, and for the next few years will focus on developing her own research designs and writing her thesis.
The exam was set by her PhD program in the Graduate School of Biomedical Sciences and Engineering, and involved writing a 6-page research proposal over the past two months, and on the day of, giving a 1-hour presentation and answering questions from her committee for up to two hours. The focus of the proposal and the presentation are a hypothetical experiment she designs on a topic that is similar to her existing research but not directly related. In that way, you can test a student’s ability to translate their existing knowledge and fact-finding skills to a totally new area and see how well they can reason through a new problem. The committee will ask students to explain their thought process, methods, and how they will assess the progress on the hypothetical project. It’s a long and arduous process, but Lola’s depth of knowledge and ability to problem-solve helped her pass with ease!
The Ishaq Lab 