A collaborative perspective article was just published in Frontiers in Microbiology, which discusses epizootic shell disease in American lobsters, the role of microbes, and the movement of microbes in an aquatic environment. Because this is a perspective article, it is more of a thought exercise than my other publications, which either report findings or review other published literature, but it was intriguing to think about animal health in the context of rapidly-changing environmental conditions and microbial communities.
I previously presented some of the microbial community data related to the larger project from which this perspective piece came about, and this research team will continue to work on analyzing data from several experiments to develop into a research article later this year.
Epizootic shell disease is becoming more prevalent on lobsters in the Gulf of Maine as waters get warmer each year.
At the time, Grace Lee was a rising senior at Bowdoin College, and accepted to my lab for the UMaine REU summer 2020 session, which was canceled. Instead, I hired Grace to perform DNA sequence analysis remotely, by independently learning data analysis following the teaching materials I had generated for my sequencing class. I invited Joelle Kilchenmann to this piece after a series of conversations about microbes and social equity, because her graduate work in Joshua Stoll’s lab focuses on lobster fishing communities in Maine and understanding the challenges they face.
Abstract: Despite decades of research on lobster species’ biology, ecology, and microbiology, there are still unresolved questions about the microbial communities which associate in or on lobsters under healthy or diseased states, microbial acquisition, as well as microbial transmission between lobsters and between lobsters and their environment. There is an untapped opportunity for metagenomics, metatranscriptomics, and metabolomics to be added to the existing wealth of knowledge to more precisely track disease transmission, etiology, and host-microbe dynamics. Moreover, we need to gain this knowledge of wild lobster microbiomes before climate change alters environmental and host-microbial communities more than it likely already has, throwing a socioeconomically critical industry into disarray. As with so many animal species, the effects of climate change often manifests as changes in movement, and in this perspective piece, we consider the movement of the American lobster (Homarus americanus), Atlantic ocean currents, and the microorganisms associated with either.
The Dairy Forage Crops Educator with the University of Maine Cooperative Extension will develop and conduct educational outreach and applied research (on farm or Experiment Station) with an emphasis on dairy forage production and quality, including regenerative pasture management. The dairy industry in New England will be the audience of focus. The individual will collaborate with the University of Vermont and their research team to conduct research and Extension education for dairy farmers in New England looking to increase forage production and utilization while facing a changing climate. Along with production, the faculty member will also address aspects of forage harvest, storage and feeding management.
Search Timeline is as follows: Review of applications to begin: April 30, 2022 Screening interviews to begin no earlier than: May 2, 2022 Final interviews to begin no earlier than: May 9, 2022 Tentative start date: June 6, 2022
Johanna Holman received the 2022 Norris Charles Clements Graduate Student Award from the University of Maine College of Natural Sciences, Forestry, and Agriculture (NSFA), for her research and academics over the last two years for her Master’s of Science in Nutrition!! This award highlights the achievements and potential for positive impact of graduate students in agriculture, is more often awarded to doctoral students who have had more years of graduate work in which to accomplish their research, give presentations, mentor undergraduates, and otherwise develop their professional skills.
Despite the setbacks and challenges of the pandemic, Johanna has been extremely productive and has done an extraordinary amount in just a year and a half (from start to the time of application submission) for her masters work. Johanna is currently writing up the results of her masters work into three manuscripts that we plan to submit to scientific journals for peer review this summer. She will defend her thesis at the end of the summer, just in time to start in September as a PhD student working with Dr. Yanyan Li and I!
Artwork by Johanna Holman
From the NSFA award page: “The Norris Charles Clements Graduate Student Award was established in the University of Maine Foundation in May 1997 for the benefit of the University of Maine, Orono, with a bequest from Laurel Clements ’48 in honor of her father, Norris Charles Clements, a distinguished Maine poultry farmer who in 1953 was honored by the University of Maine as Maine’s Outstanding Farmer. Income shall be used to provide financial assistance for rewarding outstanding graduate students in agricultural sciences and to recognize the accomplishments of graduate students whose studies have the potential to make a significant contribution to Maine agriculture. Candidates should have training and be doing research in disciplines related to Maine agriculture, such as agronomy, soil science, animal and veterinary sciences, agricultural economics, entomology, plant pathology, agricultural engineering and other disciplines the dean deems contribute significantly to the well being of Maine agriculture. Students will be chosen for awards on the basis of their high academic standing, the quality of their research and their personal integrity.”
This year, the UMaine Student Research Symposium was held in person and virtually, and undergrads and grads from the Ishaq Lab shared their research with the Maine community. You can check out the recorded presentations in the links below.
Pelletier*, 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.
Undergraduate Animal and Veterinary Science (AVS) students Natalie Sullivan (4th year), Maria Messersmith (3rd year), and Elaina Cobb (3rd year) were awarded a spring 2022 research award from the J. Franklin Witter Undergraduate Research Endowment Fund! Natalie, Maria, and Elaina will be part of a large student researcher team working on different aspects of this project over the next year, but the three of them composed the funding proposal as they have been working on this project the longest.
Background: Cryptosporidiosis, an infection caused by protozoa from the Cryptosporidium genus, often C. parvum, has emerged as a frequently reported intestinal disease of animals and humans since the 1980s when its zoonotic potential was recognized. C. parvum causes a brief diarrheal disease, which can lead to dehydration, weight loss, and, in extreme cases, death, particularly in children or neonatal animals. On farms, the disease results in intense diarrhea of neonatal calves and is associated with substantial economic losses in dairy farming worldwide as it can have long-term effects on weight gain and production efficiency. Cryptosporidiosis is transmissible via the fecal-oral route, either indirectly or directly, and C. parvum is almost always present in water and soil/bedding. There is no treatment, so disease management and prevention tend to be more focused on animal management practices involving nutrition, biosecurity, and cleanliness. This project centers around the tracking of cryptosporidium parvum in different aged dairy cattle populations at the University of Maine’s J.F. Witter Farm.
Soil samples from the farm were checked for the presence of parasites using microscopy.The calf stalls have bedding instead of soil floors, so we need to wash bedding samples to collect any protozoa that might have been left there.Cryptosporidium is most commonly spread through shared water sources so we are monitoring those.Once protozoa have been washed from the samples, the wash is put on glass slides, where dyes are used to stain the cells so we can see them using a microscope.Cows are cute but make sure you wash your hands after touching them to avoid infections.Photos from the Cryptosporidium project.
Importance/Impact: This project will track the trends and prevalence in C. parvum carriage in the Witter herd, and identify if there are certain conditions in which C. parvum is more prone to grow and multiply, especially in dairy calves. We anticipate that any findings will be used to implement new management practices for the control of Cryptosporidium parvum, specifically in bovine management, and reduce zoonosis at this farm. This project will potentially lead to making management recommendations for other farms in Maine.
Research Question, Objectives, and Hypotheses: What are the difference in disease prevalence and contamination between calves, yearlings, and adults in relation to Cryptosporidium parvum? Is infection rate due to risk of age range or animals or housing conditions?
Sarah Hosler
Master’s student, has been coordinating the project but will be defending thesis this summer and is transitioning project leadership over to Ayo
Ayodeji Olaniyi
New Master’s student Jan 2022, will be taking over project management, overseeing lab work
Natalie S.
AVS Capstone senior, graduating this May, has been collecting samples and doing microscopy since fall 2021
Maria M.
AVS Capstone junior, has been collecting samples and doing microscopy since fall 2021
Elaina C.
AVS Capstone junior, started in Jan 2022, will focus on sample collection at the farm
Jada M.
AVS Capstone junior, started in Jan 2022, will focus on sample processing in the lab
Lani P.
AVS Capstone junior, started in Jan 2022, will focus on sample processing in the lab
Sydney R.
AVS Capstone junior, started in Jan 2022, will focus on literature review
Josh F.
AVS Capstone junior, started in Jan 2022, will focus on literature review
Amatullah A.
Biology Honors, started in fall 2021, will focus on sample collection at the farm
Team Crypto in the Ishaq Lab
This project is a continuation of the pilot research that undergrad Emily Pierce, master’s student Alex Fahey, and master’s student Sarah Hosler worked on over the past two years.
I have had the pleasure of sharing my work, both Ishaq lab led and collaborative, to many venues thus far in 2022, and I am grateful to the invitations I received even though I was not able to accept all of them. These have ranged from seminar series, to student groups, to scientific conferences. Some of these events have already passed, but several are forthcoming and available by registration.
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. (invited)
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.
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
Ishaq*, S., Li, Y., Holman2, 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)
Holcomb2*, L., Coffman, J., Harrison, B., Tucker, K., Ishaq, S.L. Abstract 1080. An Overview of Three Biomedical Science Projects across Three Research Institutes. UMaine Student Research Symposium (virtual). Apr 15, 2022.
Pelletier1*, M., Taylor, T., Ishaq, S. Abstract 830. Assessing the Veterinary Needs of Rural Maine and Implementing an Effective Management Plan. UMaine Student Research Symposium (virtual). Apr 15, 2022
French1*,R., and Ishaq, S. Abstract 402. Climate Change Affects Wild Mammal Ranges and Health; Will That Also Affect Infectious Disease Exposure Risk at Maine Farms? UMaine Student Research Symposium (virtual). Apr 15, 2022.
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).
see poster below
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), April 11 – 13, 2022.
“My science journey”, invited presentation and discussion of my career path to undergraduate women in STEM, UMaine WiSTEMM group, March 28, 2021
Ishaq, S. “Moose rumen microbes and you.” The Wildlife Society Nutritional Ecology Working Group Webinar series, (virtual), March 9, 2022.
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)
120 students and faculty researchers.
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.
67 participants, 131 registrants, faculty, students, public
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)
50 participants, researchers and graduate students
Booker, Y., Ishaq, S., Levesque*, D.L. “The role of the microbiome in responses to heat stress in endotherms.” The Society of Integrative and Comparative Biology (SICB) annual meeting. Phoenix, AZ. January 3-7, 2022.
Note: an asterisk denotes the speaker if multiple authors contributed, 1 after a name denotes undergrad in the Ishaq lab, 2 after a name denotes grad in the Ishaq Lab.
The Ishaq Lab is welcoming a new master’s of science student this month: Ayodeji Olaniyi! He has a background in animal science and production, and adding research skills in animal health. While still under development, Ayo’s master’s project will involve protozoal pathogens, the gut microbiome, health, and management conditions in livestock.
Ayodeji Olaniyi
Ayodeji Olaniyi, B.S.
Master’s of Science, Animal Science
Ayodeji is a graduate student in the animal science department. An aspiring and self-motivated student, with practical experience in animal production and proper farm maintenance. Spurred by the needs to improve the production of meat/livestock in Africa and ensure good health and environmental conditions for animals. Also an Animal Science Enthusiast that seeks acquisition of knowledge and the practical use of such knowledge to bridge the gap between research findings and solving Animal production challenges. He joined the lab in 2022 tracking the trends in the spread of Cryptosporidium parvum at the Witter farm. Ayodeji is an international student from Nigeria and he is looking forward to all UMaine has to offer in this next phase of his life.
Colleagues of mine at Montana State University are looking for a graduate student in agricultural weed ecology! Details of the project, application, and contact information can be found in the file below.
Please note, this position IS NOT in the Ishaq Lab, I am distributing it on their behalf.
A scientific article led by my colleague Dr. Alaa Rabee at the Desert Research Center in Egypt was just published online and is now available! Dr. Rabee and I have been collaborating remotely on projects related to the bacteria in the rumen of camels, sheep, and cows, as Dr. Rabee’s work focuses on the isolation of bacteria which can degrade plant materials efficiently and could be used to produce biofuels. He will be spending 6 months working in my lab as a visiting scholar, which was delayed until this year because of the pandemic.
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. Article.
Abstract
Lignocellulosic biomass such as barley straw is a renewable and sustainable alternative to traditional feeds and could be used as bioenergy sources; however, low hydrolysis rate reduces the fermentation efficiency. Understanding the degradation and colonization of barley straw by rumen bacteria is the key step to improve the utilization of barley straw in animal feeding or biofuel production. This study evaluated the hydrolysis of barley straw as a result of the inoculation by rumen fluid of camel and sheep. Ground barley straw was incubated anaerobically with rumen inocula from three fistulated camels (FC) and three fistulated sheep (FR) for a period of 72 h. The source of rumen inoculum did not affect the disappearance of dry matter (DMD), neutral detergent fiber (NDFD). Group FR showed higher production of glucose, xylose, and gas; while higher ethanol production was associated with cellulosic hydrolysates obtained from FC group. The diversity and structure of bacterial communities attached to barley straw was investigated by Illumina Mi-Seq sequencing of V4-V5 region of 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes and Bacteroidetes. The dominant genera were RC9_gut_group, Ruminococcus, Saccharofermentans, Butyrivibrio, Succiniclasticum, Selenomonas, and Streptococcus, indicating the important role of these genera in lignocellulose fermentation in the rumen. Group FR showed higher RC9_gut_group and group FC revealed higher Ruminococcus, Saccharofermentans, and Butyrivibrio. Higher enzymes activities (cellulase and xylanase) were associated with group FC. Thus, bacterial communities in camel and sheep have a great potential to improve the utilization lignocellulosic material in animal feeding and the production of biofuel and enzymes.
This has been a busy year for the Ishaq Lab, which has been at UMaine since September of 2019 and has built up significant momentum in that time, despite the ongoing challenges of trying to accomplish research and education during a pandemic.
Team
The Ishaq Lab managed to find time to get a group photo early this year.
Graduate and undergraduate students are critical members of the Ishaq Lab, where they assist with or perform their own research, and are both mentored by me or are being cross-trained by me to complement the work they perform in their primary lab. A crowd of students have been in the Ishaq Lab over the course of this year, which wasn’t apparent until I tallied them for research outcomes reporting purposes, as some are partially or entirely remote, and we’ve never all gathered in one place. Partly, because of pandemic safety precautions, and partly, because of busy schedules, the entire research group had not been able to meet in person for most of the last two years, and it was only this year that we finally got a group photo. Of course, that photo was almost immediately inaccurate as we welcomed several new members this fall to add to our collective expertise.
Students mentored
09/2019-06/2020
07/2020 – 06/2021
07/2021-06/2022
Total all
9
28
24
PhD, committee member
1
2
3
MS, primary mentor
0
2
2
MS, committee member
2
3
2
MPS, primary mentor
1
1
0
Honors, primary mentor
1
2
0
Honors, committee member
0
1
1
Capstone
1
10
12
Top Scholar
0
1
1
BS, primary mentor
2
0
0
REU
1
1
1
Summary of students working in or with the Ishaq Lab, by academic year.
My dog, Izzy, started coming to campus this fall to avoid some home construction, but she immediately became part of campus life. She would come to classes and entertain and calm the students, distract Zoom meetings by trying to climb out the window behind me, and helped 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. Emily Pierce (B.S. AVS 2021) is now attending veterinary school at Kansas State, and Jade Chin (B.S. AVS 2022) is attending Glasgow University for her senior year and veterinary school as part of their accelerated training program, while Grace Lee graduated from Bowdoin College (B.S. Neuroscience, 2021) and has been working there as a research assistant. Grace is a co-author with me on a paper currently in review, and other in preparation. Tindall defended her master’s of science thesis at Montana State University in August, and has been working as a research assistant performing more plant-soil feedback research while she finishes writing up the results from her graduate work for journal publication.
Publications
We had a productive year for peer-reviewed journal publications – with 8 accepted or published – the second highest total in a year I’ve ever had. Several of these have been in development since prior to 2021, 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 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 2022.
Tindall’s first and first first-authored paper, on soil microbiomes:
Dankwa, A.S., U. Humagain, S.L. Ishaq, C.J. Yeoman, S. Clark , D.C. Beitz, and E. D. Testroet. 2021. Determination of the microbial community in the rumen and fecal matter of lactating dairy cows fed on reduced-fat dried distillers grains with solubles. Animal 15(7):100281. Article.
Ishaq, S.L., A. Hotopp, S. Silverbrand, J.E. Dumont, A. Michaud, J. MacRae, S. P. Stock, E. Groden. 2021. Bacterial transfer from Pristionchus entomophagus nematodes to the invasive ant Myrmica rubra and the potential for colony mortality in coastal Maine. iScience 24(6):102663. Article.
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.
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
Many MSE members also put together a review and perspective piece about setting research priorities:
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. 2021. Twenty important research questions in microbial exposure and social equity. mSystemsAccepted Dec 2021. Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure
The first paper from a two year collaboration with Dr. Rabee, a researcher in Eqypt who is planning to visit my lab in 2022 as part of a fellowship he was awarded.
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 ONEAccepted Dec 2021.
Presentations
The Ishaq lab and our collaborators gave virtual presentations this year to scientific audiences, as well as to grade k-12 students, to students and faculty as guest seminars, and as media/news interviews. I particularly enjoyed my chat on “Animal Microbiomes”, hosted by Sheba A-J on the WeTalkScience podcast. Students Emily Pierce, Myra Arshad, Johanna Holman, Joe Balkan, Louisa Colucci, Olivia Choi, Alice Hotopp, Sarah Hosler, and Grace Lee also gave or contributed to presentations in 2021.
Ishaq, S. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. inVIVO Planetary Health. virtual. Dec 1 – 7, 2021. (invited)
Holman* J., Ishaq S.L.., Li Y., Zhang T., Balkan J., Colucci L. Prevention of inflammatory bowel disease by broccoli-sourced and microbially-produced bioactives. Video presented at: OHS Student Led Research Panel, UC Davis; Nov 2021.
Arshad*, M., Fludgate, P., Emera Rabee, A., Ishaq, S. “Preliminary results of camel rumen microbial make up”. Council on Undergraduate Research (CUR) Research Experiences for Undergraduates (REU) Symposium. (virtual). Oct 25, 2021.
The Microbes and Social Equity Working group, “Special Session 17: “Microbiomes and Social Equity” (19205).”, Ecological Society of America 2021. (virtual). Aug 5, 2021.36.
Ishaq*, S.L., Lee, G., MacRae, J., Hamlin, H., Bouchard, D. “The effect of simulated warming ocean temperatures on the bacterial communities on the shells of healthy and epizootic shell diseased American Lobster (Homarus americanus).” Ecological Society of America 2021. (virtual). Aug 2-6, 2021. (accepted talk)
Hotopp*, A., Silverbrand, S., Ishaq, S.L., Dumont, J., Michaud, A., MacRae, J., Stock, S.P., Groden, E. “Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?” Ecological Society of America 2021. (virtual). Aug 2-6, 2021. (poster)
Pierce*, E., Hosler, S., Ishaq, S. Ideal Conditions for Cryptosporidium Attachment and Infection. UMaine Student Research Symposium (virtual). April 16, 2021. (poster)
Research
2021 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.
I’ve been developing a number of aquaculture microbiome projects which are still trying to find funding, as well as continue the data analysis on a lobster shell microbiome dataset that is part of a larger project led by Dr. Deb Bouchard at the Aquaculture Research Institute (one of the researchers on the manuscripts in review and in preparation along with Grace Lee).
One pilot study did get funded, and a collaborative research team at UMaine (Drs. Erin Grey, Jen Perry, Tim Bowden) and the Downeast Institute (Dr. Brian Beal) got a few thousand dollars to collect about 200 samples to generate some data which will help us form a better idea of what’s going on. For that project, we are interested in a particular genus of bacteria, Vibrio, which contains many species that are found in the water or associated with marine animals. Some species of Vibrio can be pathogenic, and the team is curious about which species are present during scallop aquaculture productions, when they are present, and under which circumstances.
Took a break from the massive pile of work I have to go get more Vibrio culture plates from a collaborator. This should keep us busy for awhile! pic.twitter.com/6gpE0h7XG8
This summer and fall also saw a lot of activity on a collaborative project looking at small mammals in Maine and how climate change might be affecting the animals and the microbes they carry. This project has a whole team of undergraduate researchers working together from different labs (Drs. Danielle Levesque, Pauline Kamath, and Jason Johnston at UMPI), and we were poised to collect and measure dozens of animals and process lots of feces. Unfortunately, the mice and flying squirrels we were after outsmarted us and we caught fewer than 20 animals, which is enough for us to test our laboratory methods and streamline our workflow, but not enough from which to draw any conclusions. Even without a lot of data, we still consider the project to be successful because we trained so many students on various aspects of planning and conducting research, we gathered a lot of information from previous publications and are working on a literature review, and we have gained valuable perspective for planning a follow-up to this study.
We (Drs. Yanyan Li and Tao Zhang) 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. Last December and January we ran a mouse trial that generated hundreds of samples, and we have been processing them all year! Over the fall, 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 hoping to publish the results from both studies in 2022.
Microbes and Social Equity
This was an exceptional year for the Microbes and Social Equity working group, which turned 2 years old in December, and is currently at 120 members plus several dozen newsletter subscribers! We grew so much that is was time to add Directors to the Leadership Team, to support our administration and communication needs.
In spring 2021, I organized a 14-speaker seminar series, which was attended by >300 people, and used for teaching materials at several colleges and universities. This led to a virtual symposium on “Microbes, Social Equity, and Rural Health”, June 14-18th, hosted by MSE and UMaine Medicine. This featured 15 speakers across 5 themed days with 3 plenary-style talks/day, followed by 90 min of small-group discussion led by speakers and MSE members. Participants were encouraged to “problem solve” a suggested topic or one of their own choosing to create action items that were meaningful to them, such as ideas for curricula development, identifying research needs or best practices, suggestions for engaging research in policy, and more.The symposium hosted 254 participants from 22 countries, students and researchers from various fields and career levels, Maine State legislators, and the public.
We have also been leading the development of a journal special collection in mSystems, the scope of which was developed in summer 2020 by select members of the MSE working group, and which has welcomed its first few contributions this year. The inaugural piece was one written by 35 MSE group members which introduced the group, established our mission statement, and outlined our goals.
We hosted a panel discussion at the 2021 Ecological Society for America meeting, and plan to host more conference sessions in 2022. In 2022, we will be hosting a spring seminar series, as well as a summer symposium which is still under development. We’ll be adding the rest of the contributions to the mSystems special collection, and hopefully some collaborative projects! There will also be a few presentations at scientific conferences.
The website gained a phenomenal amount of traffic this year, largely due to MSE, with more than 10,000 visitors and more than 25,000 views! I published more than 50 blog posts, as well as a few dozen more that were advertising events.
Total visitors and views by year.
We had visitors from 125 countries around the globe!
Number of website views per country of origin.
Looking ahead to 2022
I’ll be starting 2022 early with proposal writing, drafting manuscripts, and teaching three classes (I offered to teach the third as overload because we are understaffed). I will be undergoing my third year review this spring, which is a milestone in my tenure-track journey. And, I already have a handful of presentations lined up:
Ishaq, S. ”Microbes at the nexus of environmental, biological, and social research. 2nd Rhode Island Microbiome Symposium, in person, University of Rhode Island Kingston, RI, January 14, 2022. (invited plenary)
Ishaq, S. et al. “TBD” Dartmouth Molecular Microbiology and Pathogenesis (M2P2), February 24-25, 2021.
Ishaq, S. “Moose rumen microbes and you.” The Wildlife Society Nutritional Ecology Working Group Webinar, March 9, 2022.
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. (invited)
American Society for Microbiology (ASM) Microbe 2022 special session: “CTS16 (PPS) Cross-Track Symposium: Microbes and Social Equity: the Microbial Components of Social, Environmental, and Health Justice”. Washington, D.C. June 9-13, 2022. Organized by Ishaq, S.L. and featuring Drs. Ari Kozik, Carla Bonilla, and Monica Trujillo.
The Ishaq Lab 