The Ishaq Lab is ecstatic to welcome Alexis Kirkendall for the third time — this time as a PhD student of Microbiology!!
Alexis Kirkendall originally joined the lab in summer 2022 for ten weeks through the Research Experience for Undergraduates program through the NRT Initiative for One Health & the Environment. During that time, she learned various laboratory techniques related to microbiology and genomics, and participated in several projects which investigated the microbes associated with several species of livestock. Alexis picked these up so quickly that she acted as project manager for one of them and trained other undergraduates and a graduate student in the lab. Within a few weeks of arriving here, Alexis was working independently in the lab, and we began talking about her joining the lab for a graduate program.
Alexis Kirkendall processing microscope slides.Alexis Kirkendall collected samples from calves.
Over the 2022/2023 academic year, Alexis continued to work with me remotely as she went back to continue her bachelor’s at Heidelberg College. This included data analysis and visualization of RNA transcriptomic data from the rumen of camels, as well as presenting results from her summer work at the UMaine REU student symposium, the Heidelberg College student research symposium, and a national conference:
Kirkendall*, A., Ishaq, S. Taking on Multiple Research Projects in a NSF Research Experience for Undergraduates (REU) Summer Program as a Disabled Undergraduate Student. ABRCMS annual meeting, Anaheim, CA, November 9-12, 2022.
In summer 2023, she again joined the lab as an undergraduate research assistant, where she worked with a team of undergraduate and graduate students working on anaerobic culturing and growth trials for bacteria isolated from mice consuming a broccoli sprout diet, to determine their activity for converting a dietary compound into an anti-inflammatory to resolve Inflammatory Bowel Disease. She got our robotic liquid handler programmed for that project, too! The summer work laid the groundwork for the dissertation work she’ll be completing with me.
Alexis Kirkendall, Jaymie Sideaway, Aakriti Sharma, Sue Ishaq, Johanna Holman, and Lilian Nowak.
Alexis graduated early (Dec 2023) and is rejoining #TeamBroccoli to work on how different cooking preparations affects the way gut microbes turn an inactive component into an ani-inflammatory in the intestines, as a way to reduce symptoms in Inflammatory Bowel Disease. We have been benchmarking some of those gut microbes for their capacity for GLR metabolism to produce SFN, and our long-term goal is to develop a dietary preparation of broccoli sprouts and a probiotic which have therapeutic effects against IBD in humans.
In addition to the lab work and research, Alexis has also been heavily involved in the Microbes and Social Equity working group. She participated in MSE’s symposium in 2022 and 2023, acting as a notetaker to facilitate discussions between invited speakers, MSE members, and other audience members, and organizing of the meeting by helping to create agendas and notes documents on behalf of the session organizers. In 2024, she’ll continue to help me curate events and develop content for MSE.
The American Society for Microbiology is an internationally recognized scientific society that promotes research, education, and policy related to microbiology in all aspects of our lives. I’ve been a member since 2011, have been to several meetings, and have published several times in ASM journals, and have spent quite a bit of time envisioning how scientific societies can foster the next generation of researchers. And now…
I’m eager to learn from ASM leaders about how best to support my scientific community! I hope to use my time on the board to identify ways that ASM can remove barriers to participating in science that early-career researchers face. You can find info on next leadership team here.
I’ll be hosting a webinar later today in the mSystems Thinking Series, which focuses on the topic of “Microbes and Sexual Health”. Hear from experts in microbiology and human health, and join the conversation on how to engage in this research with empathy and inclusiveness.
I’ll be hosting a webinar in the mSystems Thinking Series, which focuses on the topic of “Microbes and Sexual Health”. Hear from experts in microbiology and human health, and join the conversation on how to engage in this research with empathy and inclusiveness.
Dec 7, 2023, 4 pm ET.
The webinar was free with registration. You can check out the recorded webinar on the mSystems Youtube channel here.
Speakers:
Gaea Daniel, Ph.D., RN, assistant professor, Nell Hodgson Woodruff School of Nursing, Emory University.
Marisol Dottie Dothard, Ph.D. student, University of California, San Diego.
The American Society for Microbiology is an internationally recognized scientific society that promotes research, education, and policy related to microbiology in all aspects of our lives. I’ve been a member since 2011, have been to several meetings, and have published several times in ASM journals, and have spent quite a bit of time envisioning how scientific societies can foster the next generation of researchers. And now… I’m on the ballot for an Early-Career At-Large positon on their Board of Directors! If you are a member of ASM, you are able to vote for the next leadership team, whose profiles can be found here, and will have received an email link.
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.
Marissa completed her undergraduate at the University of Maine in 2021, earning a BS in Microbiology and a BS in Cellular/Molecular Biology, and after graduating worked in the field of public health at UMaine’s Margaret Chase Smith Policy Center. She’s been crushing it since joining the lab in early 2023, including contibuting to the two papers listed below, being awarded a One Health and the Environment NRT Fellowship 2023 – 2024 at UMaine, and now, a research award from the Bioscience Association of Maine!!
Lola entered as a rotating first-year GSBSE student in March 2022, and declared the Ishaq Lab her dissertation lab soon after, where she has been performing 16s data analysis for other ongoing lab projects, comparing gut microbiomes of mouse models of Inflammatory Bowel Disease with broccoli as a dietary treatment. Lola was awarded a One Health and the Environment NRT Fellowship 2022- 2024 here at UMaine. She led the data analysis on a paper using a Crohn’s Disease mouse model for innovate diet-microbe research.
Johanna was first author on a paper that was recently published, and contributed to a second paper accepted (details soon)!
Johanna Holman, B.S., M.S.
Doctor of Philosophy student
Johanna joined the lab in fall 2020 to investigate the effects of diet on the gut microbiome, and on host-microbial interactions. For the past several years, she has been working with Drs. Tao Zhang and Yanyan Li, and her project will combine her previous work on the nutritional biochemistry of broccoli with effects on gut microbes. She obtained her master’s in nutrition in summer 2022, and returned to the Ishaq and Li labs for her PhD! She won the 2022 Norris Charles Clements Graduate Student Award and the 2020-2021 University of Maine Graduate Student Employee of the Year. She led a large mouse project which was recently published, and led much of the lab work for a second paper that was just accepted.
Alexis is returning soon as PhD student in Microbiology!
Alexis Kirkendall
Undergraduate Researcher
Alexis is from Ohio and is about to graduate a semeser early in Biology at Heidelberg University. She joined the lab through the Summer 2022 REU, continued her work remotely, and returned to Maine in summer 2023 as a research assistant for several projects related to gut microbes, diet, and Inflammatory Bowel Disease. She was just accepted into the microbiology program at UMaine!!
Esther joined the lab!
Esther Alaba
Doctorate of Philosophy candidate
Esther has won several awards for combining mechanistic and functional tools to investigate dietary interventions in managing metabolic diseases. Her teaching experience includes Basic Physiology, Anatomy, and Experimental Physiology courses. She is passionate about Girls’ Education and Empowerment and currently mentors several young women towards successful career development.
Her desire to utilize bioinformatics tools for nutritional therapy brought her to Ishaq’s lab. She currently works on human and mouse data to identify the microbiome and metabolomic pathways involved in the ameliorative effects of broccoli sprouts during IBD.
I was recently featured in the Design Observer Twenty for my work on Microbes and Social Equity! The Design Observer is turning 20 this month, so they interviewed 20 people who have been changing the way the world looks at health, wellbeing, sustainability, and designing for a more equitable future.
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. You can read about the whole project here, with links to other resources.
The Premise
Designed by Johanna Holman
Broccoli sprouts are very high in a compound called glucoraphanin. When glucoraphanin comes in contact with the myrosinase enzyme, also found in the sprouts, it is transformed into a compound that acts an an anti-inflammatory in people!
If you eat raw sprouts, 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 the compound, and produce the anti-inflammatory 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 Mouse work
In the winter of 2020-2021, we ran a 40-day study with 40 mice housed at UMaine. The mice were divided into 4 groups: “control” which ate the mouse chow, “control+DSS” which ate the mouse chow and had colitis induced by adding DSS (a salt laxative) to their drinking water, “broccoli” which ate the mouse chow with steamed broccoli sprouts mixed in, and “broccoli+DSS” which ate the mouse chow/steamed broccoli sprouts diet and had colitis induced by adding DSS (salt laxative) to their drinking water. This work was led by Johanna Holman, who was a master’s student at the time; Lousia Colicci, who was an undergrad at Husson University at the time and is applying to medical schools now; Dorein Baudewyns, who was an undergrad at Husson University at the time and is completing a graduate program in Psychology at UMaine; and Joe Balkan, who was completing his senior year of high school at the time and has since begin an undergrad degree in Biology at Tufts University where he is preparing for medical school.
Johanna Holman, graduate researcher in the Ishaq LabLouisa Colucci.Dorien Baudewyns, undergraduate researcher at Husson UniversityJoe Balkan, undergraduate researcher at Tufts University, performing culturing of bacteria at the anaerobic chamber.
The mice were weighed regularly and fecal samples assessed for blood (signs of colitis). At the end of the study, the mice were euthanized so we could study the bacteria in parts of the intestines that we can’t access in humans. We used as few mice as possible, and got as much information from this study as possible, to do as much good as we can with their sacrifice.
The Health Benefits
As we’d hoped, the broccoli+DSS mice that were eating the broccoli sprouts that were given colitis did much better than the control+DSS group who ate mouse chow during their colitis. The broccoli+DSS mice were able to keep gaining weight as they grew, had better consistency of their stool, and had lower amounts of proteins and other metabolities in their blood which indicate inflammation (lower cytokines and lipocalin). Those graphs are shown in the paper.
The Gut Microbes
We found a lot of interesting things with the microbial communities that were living in different parts of the intestines, but the most exciting was that broccoli sprouts in the diet helped microbial communities stay alive in their original gut locations even during colitis! Certain microbes like to live in particular places in our intestines based on where different ingredients in our diet get processed, or the local environment (like how acidic the intestinal neighborhood is), and this is called biogeography.
In the graph below, our control group mice (eating chow) or the broccoli group (eating chow plus sprouts), we see that microbial communites in the small intestines clustered away from the microbial communities in the large intestines.
The DSS salt laxative, and ulcerative colitis, wreak havoc on gut microbes because they cause physical damage to the lining of the intestine, which where many microbes that can be useful to us live on or near. When we induced colitis in mice that were eating mouse chow (control+DSS group), the damage to the intestines caused a loss to some of the microbes living in different places. The remaining microbes that could survive these tough conditions were basically the same ones regardless of where we we looked in the intestines.
But, if mice had colitis and were eating broccoli sprouts (broccoli+DSS), the microbes were able to survive in their original locations and preserved biogeography! This is important because where microbes live in the gut may determine if the beneficial things they make can help resolve IBD symptoms in specific locations in the gut.
Image by Johanna Holman, graph from the paper.
The Spatial Location of GLR-digesting-genes
Bejamin and Timothy Hunt are undergraduates in Biology who have been working on bioinformatics in the Ishaq Lab since December 2022 after completing Sue’s DNA Sequencing Data Analysis Class. They joined the DSS project to provide in-depth analysis on some of the sequences which matched bacteria that are known to convert GLR into the anti-inflammatory SFN, as well as analyze data comparing numbers of genes known to be involved in the process.
Cropped figure from the paper, made by Benjamin and Timothy.
Benjamin Hunt
The study of the bioproduction of SFN and its mucosal and luminal activity benefited from the biogeographical analysis of this study. It was interesting to note the extreme dominance of a Bacteroides species in the broccoli treatments. B. thetaiotaomicron was indicated based on BLASTN analysis and an evaluation of matching species but was not directly suggested by the dada-Silva taxonomy assignment. The indication of B. thetaiotaomicron suggested analyzing the presence of the operon BT2159-BT2156, which was generally minimally present (<100) but at relatively high counts (>100,000) in some samples. Significantly, the operon was found at locations where no Bacteroides were identified. We continue to reflect on the similarities and differences in the biogeography of bacterial abundance and operon presence highlighted in the different treatments of this study.
Benjamin and Timothy Hunt
The Next Steps
As part of this project, we cultured hundreds of bacteria from the intestines of mice to try and isolate some of the ones that turn glucroraphanin into sulforaphane. We have a large team of students and researchers participating on the culturing work, some of whom are pictured here. We’ll be providing plenty of updates on that project as we continue to process the bacteria this fall!
Johanna M. Holman1, Louisa Colucci2, Dorien Baudewyns3, Joe Balkan4, Timothy Hunt5, Benjamin Hunt5, Marissa Kinney1, Lola Holcomb6, Allesandra Stratigakis7, Grace Chen8, Peter L. Moses9,10, Gary M. Mawe9, Tao Zhang7, Yanyan Li1*, Suzanne L. Ishaq1*
1 School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469 2 Department of Biology, Husson University, Bangor, Maine, USA 04401 3 Department of Psychology, University of Maine, Orono, USA 04469 4 Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts, USA 02155 5 Department of Biology, University of Maine, Orono, Maine, USA 04469 6 Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469 7 School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790 8Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA 481099Departments of Neurological Sciences and of Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 0540110 Finch Therapeutics, Somerville, Massachusetts, USA 02143
Abstract: Inflammatory Bowel Diseases (IBD) are devastating conditions of the gastrointestinal tract with limited treatments, and dietary intervention may be effective, and affordable, for managing symptoms. Glucosinolate compounds are highly concentrated in broccoli sprouts, especially glucoraphanin, and can be metabolized by certain mammalian gut bacteria into anti-inflammatory isothiocyanates, such as sulforaphane. Gut microbiota exhibit biogeographic patterns, but it is unknown if colitis alters these or whether the location of glucoraphanin-metabolizing bacteria affects anti-inflammatory benefits. 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 sodium sulfate (DSS) in drinking water over a 34-day experiment to simulate chronic, relapsing ulcerative colitis. We monitored body weight, fecal characteristics, lipocalin, serum cytokines, and bacterial communities from the luminal- and mucosa-associated populations in the jejunum, cecum, and colon. Mice fed the broccoli sprout diet with DSS treatment performed better than mice fed the control diet with DSS, including significantly more weight gain, lower Disease Activity Indexes, lower plasma lipocalin and proinflammatory cytokines, and higher bacterial richness in all gut locations. Bacterial communities were assorted by gut location, but were more homogenous across locations in the control diet + DSS mice. Importantly, our results showed that broccoli sprout feeding abrogated the effects of DSS on gut microbiota, as bacterial richness and biogeography were similar between mice receiving broccoli sprouts with and without DSS. Collectively, this supports the protective effect of steamed broccoli sprouts against dysbiosis and colitis induced by DSS.
Importance: Evaluating bacterial communities across different locations in the gut provides a greater insight than fecal samples alone, and provides an additional metric by which to evaluate beneficial host-microbe interactions. Here, we show that 10% steamed broccoli sprouts in the diet protects mice from the negative effects of dextran sodium sulfate induced colitis, that colitis erases biogeographical patterns of bacterial communities in the gut, and that the cecum is not likely to be a significant contributor to colonic bacteria of interest in the DSS mouse model of ulcerative colitis. Mice fed the broccoli sprout diet during colitis performed better than mice fed the control diet while receiving DSS. The identification of accessible dietary components and concentrations that help maintain and correct the gut microbiome may provide universal and equitable approaches to IBD prevention and recovery, and broccoli sprouts represent a promising strategy.
Acknowledgements: All authors have read and approved the final manuscript. The authors thank Jess Majors, University of Maine, for her kind and detailed care of the mice during the trial, and for Ellie Pelletier for her informal review of the manuscript. 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) which supported Johanna Holman; 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. 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 through the UMaine Graduate School of Biomedical Sciences and Engineering.
I’ve been a researcher since Juy 2010, when I started graduate school, and my first peer-reviewed journal article was accepted in 2012. This summer, I reached 50 peer-reviewed publications, including research papers and reviews. Since I started publishing, I’ve been in grad school, two one-year postdoc positions, one two-year research assistant professor position, and one four-year-and-counting assistant professor position, and my research areas of focuses have shifted 5 or 6 times since then to keep pace with the job I was in at the time. To capture that diversity, I made a word cloud of my publication list, including authors, titles, and journal names:
Top keywords:
Unsurprisingly, most of my top keywords include the microbes I’m focusing on (bacterial), the animals I’ve worked with (moose, Alces), the sample types I’ve worked with (rumen, soil), and the methodology I use (seqeuencing).
Top co-authors:
None of this would have been possible without hundreds of researchers that I have worked with over the years. Here are a few of the names that pop up in theat wordcloud because I have published so often with them:
Carl Yeoman, Montana State University, who was my post-doc advisor for a year and who I’ve continued to publish with on various projects. We’ve co-authored 11 papers!!
Andre Wright, my PhD avisor, who has since moved into non-research roles, also with 11 co-authored papers!!
Fabian Menalled, Montana State University, who was my post-doc advisor for a year and who I collaborated with for many years on projects which sprung from that first year. We have 7 co-authoured papers!
Jean MacRae, University of Maine, and I have collaborated on a handful of different projects since I joined UMaine and have co-authored 4 papers with another currently in review.
Full list of Research Articles (38) and Reviews (12):
1 undergraduate student I mentored, 2 graduate student I mentored
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. mSystems7(1): e01240-21.Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure. (review)
Ishaq, S.L., Parada, F.J., Wolf, P.G., Bonilla, C.Y., Carney, M.A., Benezra, A., Wissel, E., Friedman, M., DeAngelis, K.M., Robinson, J.M., Fahimipour, A.K., Manus, M.B., Grieneisen, L., Dietz, L.G., Pathak, A., Chauhan, A., Kuthyar, S., Stewart, J.D., Dasari, M.R., Nonnamaker, E., Choudoir, M., Horve, P.F., Zimmerman, N.B., Kozik, A.J., Darling, K.W., Romero-Olivares, A.L., Hariharan, J., Farmer, N., Maki, K.A., Collier, J.L., O’Doherty, K., Letourneau, J., Kline, J., Moses, P.L., Morar, N. 2021. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. mSystems 6:4. Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure. (review)
Zeng, H., Safratowich, B.D., Liu, Z., Bukowski, M.R., Ishaq, S.L. 2021. Adequacy of calcium and vitamin D reduces inflammation, β-catenin signaling, and dysbiotic Parasutterella bacteria in the colon of C57BL/6 mice fed a Western-style diet. Journal of Nutritional Biochemistry 92: 108613.Article.
Horve1, P.F., Dietz, L., Ishaq, S.L., Kline, J., Fretz, M., Van Den Wymelenberg, K. 2020. Viable bacterial communities on hospital window components in patient rooms. PeerJ 8:e9580.
Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Dryland cropping systems, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities. mSphere 5:e00340-20.
Garcia-Mazcorro, J., Ishaq, S.L., Avila-Jaime, B., Rodriguez-Herrera, M.V., Kawas, J.R., Nagaraja, T.G. 2020. Are there any native Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits. Animal 14(1):22-30. (review)
Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Soil bacterial communities of wheat vary across the growing season and among dryland farming systems. Geoderma 358(15):113989.
Ishaq, S.L., Rapp1, M., Byerly1, R., McClellan1, L.S., O’Boyle1, M.R., Nykanen1, A., Fuller1, P.J., Aas1, C., Stone1, J.M., Killpatrick1, S., Uptegrove1, M.M., Vischer1, A., Wolf1, H., Smallman1, F., Eymann1, H., Narode1, S., Stapleton, E., Cioffi, C.C., Tavalire, H. 2019. Framing the discussion of microorganisms as a facet of social equity in human health. PLoS Biology 17(11): e3000536. Microbiomes Across Systems special issue. Article. (review)
Velazquez1, S., Griffiths1, W., Dietz, L., Horve1, P., Nunez1, S., Hu, J., Shen, J., Fretz, M., Bi, C., Xu, Y., Van Den Wymelenberg, K.G., Hartmann, E.M., Ishaq, S.L.2019. From one species to another: A review on the interaction of chemistry, microbiology, and occupancy in the built environment. Indoor Air 26(6):875-1049. (review). Top 10% most downloaded papers from 2018 – 2019, and 2019 – 2020.
Velazquez1, S., Bi, C., Kline, J., Nunez1, S., Corsi, R., Xu, Y., Ishaq, S.L. 2019. Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community. PeerJ 7:e8147.
Stenson, J., Ishaq, S., Laguerre, A., Loia, A., MacCrone1, G., Mugabo, I., Northcutt, D., Riggio, M., Barbosa, A., Gall, E., Van Den Wymelenberg, K. 2019. Occupant Experience of a Mass Timber Office Building: Monitored and Perceived. Buildings 9:142.
Seipel, T., Ishaq, S.L., Menalled, F.D. 2019. Agroecosystem resilience is modified by management system via plant–soil feedbacks.Basic and Applied Ecology 39:1-9.
Ishaq, S.L., Lachman2, M.M., Wenner, B.A., Baeza, A., Butler, M., Gates, E., Olivo, S., Buono Geddes, J., Hatfield, P., Yeoman, C.J. 2019. Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed. PLoS ONE 14(6): e0215797.
Ishaq, S.L., Page, C.M., Yeoman, C.J., Murphy, T.W., Van Emon, M.L., Stewart, W.C. 2019. Zinc-amino-acid supplementation alters yearling ram rumen bacterial communities but zinc sulfate supplementation does not. Journal of Animal Science 97(2):687-697.
Horve1, P.F., Lloyd1, S., Mhuireach, G.A., Dietz, L., Fretz, M., MacCrone1,G., Van Den Wymelenberg, K., Ishaq, S.L.2019. Building Upon Current Knowledge of Indoor Microbiology to Construct the Next Era of Research into Microorganisms, Health, and the Built Environment. Journal of Exposure Science and Environmental Epidemiology 30:219–235. Healthy Buildings special issue. (review)
Yeoman, C.J. and Ishaq, S.L.*, Bichi, E., Olivo, S.K., Lowe, J., Aldridge, B.M. 2018. Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract. Scientific Reports 8:3197. *authors contributed equally. Article
Seshadri, R., Leahy, S.C., Attwood, G.T., The, K.H., Lambie, S.C., Eloe-Fadrosh, E., Pavlopoulos, G., Hadjithomas, M., Varghese, N., Hungate1000 project collaborators, Perry, R., Henderson, G., Creevey, C.J., Terrapon, N., Lapebie, P., Drula, E., Lombard, V., Rubin, E., Kyrpides, N., Henrissat, B., Woyke, T., Ivanova, N., Kelly, W.J. 2018.Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnology 36:359-367.
Zeng, H., Ishaq, S.L., Liu, Z., Bukowski, M. 2018. Colonic aberrant crypt formation accompanies an increase of opportunistic pathogenic bacteria in C57BL/6 mice fed a high-fat diet. Journal of Nutritional Biochemistry 54:18-27.
Ishaq, S.L., AlZahal, O., Walker, N., McBride, B. 2017. Modulation of sub-acute ruminal acidosis by active-dry yeast supplementation and its effect on rumen fungal and protozoal populations in liquid, solid, and epimural fractions.Frontiers in Microbiology 8:1943.
Ishaq, S.L., Yeoman, C.J, Whitney, T.R. 2017. Effects of ground redberry juniper and urea in DDGS-based supplements on ewe lamb rumen microbial communities. Journal of Animal Science 95(10):4587-4599.
Perea1, K., Perz, K., Olivo, S.K., Ishaq, S.L., Williams, A., Lachman, M., Thompson, J., Yeoman, C.J. 2017. Feed efficiency phenotypes involve changes in ruminal, colonic, and small intestine-located microbiota. Journal of Animal Science 95(6):2585-2592.
Ishaq, S.L., Johnson, S.P., Miller, Z.J., Lehnhoff, E.A., Olivo, S.K., Yeoman, C.J., Menalled, F.D. 2017. A living soil inoculum increases soil microbial diversity, crop and weed growth using soil from organic and conventional farms in northeastern Montana. Microbial Ecology 73: 417.
Ishaq, S.L. 2017. Plant-Bacteria Interactions in Agriculture and the Use of Farming Systems to Improve Diversity and Productivity. AIMS Microbiology 3(2): 335-353. (review)
Feng, W., Minor, D., Liu, M., Li, J., Ishaq, S.L., Yeoman, C., Lei, B. 2016. Null Mutations of Group A Streptococcus Orphan Kinase RocA: Selection in Mouse Infection and Comparison with CovS Mutations in Alteration of in vitro and in vivo Protease SpeB Expression and Virulence. Infection and Immunity 25:30-36.
Zeng, H., Ishaq, S.L., Zhao, F-Q., Wright, A-D.G. 2016. Colonic inflammation accompanies an increase of b-catenin signaling Lachnospiraceae/Streptococcaceae in the hind-gut of high-fat diet-fed mice. Journal of Nutritional Biochemistry 35:30-36.
Salgado-Flores, A., Hagen, L.H., Pope, P.B., Ishaq,S.L., Wright, A-D.G., Sundset, M.A. 2016. Intake of a lichen-based diet altered the rumen and cecum microbial profiles in Norwegian reindeer (Rangifer tarandus tarandus). PLoS ONE 11(5).
Ishaq, S.L., Moses, P.L., Wright, A-D.G. 2016. The pathology of methanogenic archaea in human gastrointestinal disease. In: The Gut Microbiome – Implications for Human Disease. Mozsik, G. (ed.). InTech. Pp. 19-37. (review)
Ishaq, S.L., Kim1, C.J., Reis1, D.,Wright, A-D.G. 2015. Fibrolytic bacteria isolated from the rumen of North American moose (Alces alces) and their potential as a probiotic for ruminants. PLoS ONE 10:12.
Ishaq, S.L., Sundset, M.A., Crouse, J., Wright, A-D.G. 2015. High-throughput DNA sequencing of the moose rumen from different geographical locations reveals a core ruminal methanogenic archaeal diversity and a differential ciliate protozoal diversity. Microbial Genetics 1(4):mgen.0.000034.
Ishaq, S.L., Wright, A-D.G. 2015. Wild Ruminants. In: Rumen Microbiology – Evolution to Revolution. AK Puniya, R Singh, DN Kamra (eds). Springer India. Pp. 37-45. (review)
St-Pierre, B., Cersosimo, L.M., Ishaq, S.L., Wright, A-D.G. 2015. Toward the identification of methanogenic archaeal groups as targets of methane mitigation in livestock animals. Frontiers in Microbiology 6:776. (review)
Ishaq, S.L., Wright, A-D.G. 2014. Design and validation of four new primers for next-generation sequencing to target the 18S rRNA gene of gastrointestinal ciliate protozoa. Applied and Environmental Microbiology 80(17):5515-5521.
Ishaq, S.L., Wright, A-D.G. 2014. High-throughput DNA sequencing of the ruminal bacteria from moose (Alces alces) in Vermont, Alaska, and Norway. Microbial Ecology 68(2):185-195.
Ishaq, S.L., Wright, A-D.G. 2012. Insight into the bacterial gut microbiome of the North American moose (Alces alces). BMC Microbiology 12:212.
The Ishaq Lab 