The speaker lineup is set for the third day of the July 2022 MSE virtual symposium, which is focused on “Transforming your research for policy engagement”. This session will feature three talks featuring researchers who have experience bringing research to the public and to legislative bodies. So often, the positive outcomes of research are limited because it can be difficult to get the word out to people who can put our results into practice. Our hope is that attendees for this session learn from different perspectives how to write their research to inform the general public, professionals in healthcare, or policy makers.
Mallory Choudoir, Ph.D. Soil microbial ecologist. Postdoctoral Researcher at University of Massachusetts Amherst. Assistant Professor and Extension Specialist at North Carolina State University September 2022.
Amali Stephens, PhD Student, Interdepartmental Microbiology, Iowa State University
Scope: Microbiomes drive processes in all environments and are intimately intertwined with all aspects of our lives. Despite the central role of microbes in shaping systems, microbial researchers are often detached from shaping policies related to conservation, public health, land use, environmental justice, climate and other areas of intersection. Policy engagement is not typically included in the academic training of microbiome researchers, and there is a need for greater coordination between policy needs and microbial research. This session will explore integrated, collaborative approaches to research and policy making.
Learning Objectives of Session: Attendees will discuss 1) how to develop research in collaboration with policy needs, 2) policy levels and types (government, private), 3) how to identify stakeholders, and 4) how to communicate your research to policymakers.
Format of talks: Three 30-min lecture-style talks will describe interdisciplinary research outcomes which transcend typical academic endpoints and engage in shaping policy.
Format of breakout rooms: Each room will create a policy brief outline or ideas list around a particular topic area (e.g. environmental restoration) to help audience members group by discipline.
Session Speakers: In development, details provided soon!
Dr. Caitlyn Hall, PhD., Assistant Professor of Practice, University of Arizona
The speaker lineup is set for the second day of the July 2022 MSE virtual symposium, which is focused on “Blending biological, social, and humanities writing”. This session will feature one talk and one panel discussion, featuring researchers who have published, reviewed, and edited interdisciplinary writing and appreciate the difficulty that many microbiome researchers face: getting their work published when it does not fit a typical experimental layout. Our hope is that attendees for this session learn from different perspectives how to write across disciplines, find the right journal and pitch the relevancy of their manuscript to the journal’s scope, how to find reviewers with disparate professional backgrounds (for example microbiology and legal policy), and more.
Emily Wissel, Ph.D. candidate, Emory University. MSE Director of Resource Dissemination
Scope: Interdisciplinary experimental designs have been called for in research, but finding a publication venue can be tricky when manuscripts or presentations are deemed not discipline-specific, or are labeled opinion instead of research. This session will explore common gatekeeping problems of interdisciplinary research, cross-disciplinary writing categorization discussions (i.e. theoretical framing, etc.), and writing strategies and publication venues to make the most of your work.
Learning Objectives of Session: Attendees will become familiar with different expectations within research design/publishing across fields, and learn about tangible suggestions from research publishers. Audience members should walk away with more confidence in interdisciplinary publishing.
Format of talks: This will feature a 30-min plenary topic to introduce the concept that theory in psychology/philosophy is regarded as opinion in the natural sciences, followed by 1 hour of a panel of research journal editors to discuss flexible publication guidelines.
Format of breakout rooms: Each room creates a document, and each room has a designated topic area (e.g. environmental restoration) to help audience members group by discipline
“Crossing boundaries, building bridges: some reflections on interdisciplinary writing.”
After which, the Speaker will be joined by additional Panelists to discuss interdisciplinary research, challenges, and opportunities.
Dr. Susan L. Prescott, MD, PhD, FRACP. President, inVIVO Planetary Health @ the Nova Institute for Health, Baltimore, USA; Director, ORIGINS PROJECT Telethon Kids Institute; Professor of Paediatrics, UWA Medical School; Paediatric Immunologist, Perth Children’s Hospital; Editor in Chief, Challenges journal.
Dr. James Stegen, PhD., Physical & Computational Sciences Directorate, Pacific Northwest National Laboratory
Dr. Michela Gambino, PhD. Assistant Professor at the Department of Veterinary and Animal Sciences, University of Copenhagen; mSystems editor
12:30 – 14:15 Introduction, Speaker, and Panel discussion
14:15 – 14:30 Break
14:30 – 16:00 Breakout room discussions based on skills development, in smaller groups
Pitching your paper to the right journal
Finding and directing reviewers
“Ask a philosopher!”
Prior to this session, you may want to watch these recorded talks:
After two years of postponement, the Ishaq Lab is excited to welcome Dr. Alaa Rabee as a Visiting Researcher from now until December of this year!! This is made possible by a prestigious award to Dr. Rabee from the Central Department of Missions at the Ministry of Higher Education, Egypt, which fosters research collaboration between Egypt and the U.A.
Dr. Rabee joins us from the Desert Research Institute in Cairo, Egypt, where his work focus on researching microbial communities in the digestive tract of ruminants and how they can be used for animal production, bioengineering, and sustainable development.
Last year, Alaa and I published our first collaborative paper together, based on his work on microbial enzymes from the rumen of sheep and camels and potential for use in biofuel production. We are also working on another, based on microbial activity (transcriptomics) in the rumen of camels on different diets. That project has engaged two undergraduate students in data visualization, including Myra Arshad who started in my lab as an REU student last summer.
During his six month stay, he’ll be working with rumen microbes from various livestock, as well as giving seminars and sharing his experience in research.
The speaker lineup is set for the fifth (and final) day of the July 2022 MSE virtual symposium, which is focused on “MSE Education Practices and Curriculum Design”. This session will feature three talks featuring educators who have brought sociology into their microbiome courses, and vice versa, and who have experience creating out-of-the-box curricula to engage students in learning while helping them to see themselves as scientists. Our hope is that attendees for this session learn from different perspectives how to creatively present microbiology courses which situate learning about the microbiome with learning about social and environmental systems.
Erin Eggleston, PhD, Assistant Professor of Biology, Middlebury College.
Monica Trujillo, Ph.D., Associate Professor, of Biology Queensborough Community College, The City University of New York
Carla Bonilla, Ph.D., Associate Professor, University of San Diego
Scope: Curriculum which blends disciplines is highly engaging, and can be used to teach complex concepts, and can help students combine their existing cultural and social identities with their growing researcher identity. However, creating an interdisciplinary curriculum can be challenging. This session frames educational conversations in MSE, and gives perspectives on creating courses that blend microbiome and social sciences for different levels of education.
Learning Objectives of Session: Attendees will 1) identify successes and barriers to entry for MSE curriculum at different education levels (K-12, UG, grad, general public), 2) Share ways in which we incorporate MSE in our curricula (i.e. assignments, class period, multi-day module, full course, etc.); 3) develop ideas for further curriculum design for their own courses.
Format of talks: Three 30-min lecture-style talks from education practitioners who have successfully built courses around MSE topics, including an outline of learning goals, approach to course, lessons learned/challenges, and more.
Format of breakout rooms: Each room creates a lesson plan outline, and each room has a designated topic area (e.g. human microbiome equity) to help audience members group by teaching discipline.
Session Speakers: In development, details provided soon!
Dr. Ally Hunter, PhD., Lecturer, iCONS Program & Postdoctoral Fellow, Center for Youth Engagement, University of Massachusetts, Amherst. Part of NSF Project RAISE (Reclaiming Access to Inquiry Science Education for Incarcerated Learners), and NSF Project INSITE (INtegrating STEM Into Transition Education for Incarcerated Youth).
The speaker lineup is set for the first day of the July 2022 MSE virtual symposium, which is focused on “Context-aware experimental designs”. The three talks, featuring a total of 5 researchers, will present perspectives on the human microbiome and studying it within broader contexts to better understand our interactions with microbes. Our hope is that attendees for this session learn from different perspectives how to more creatively design or analyze their research to account for the effects that social policy and local environment can have on microbial exposures.
Scope: Microbiome research often uses broad categorical factors as proxy factors for complex social or environmental contexts, but these can ignore or obscure underlying trends. This session will unpack proxy terms like race, Western diet, dysbiosis, rural/urban, and more, to differentiate what variables we actually want to measure and how to accomplish this in data collection and analysis. This session will also discuss how to communicate microbiome results in relation to broader contexts of lived experiences, rather than attributing results to broad proxy categories.
Learning Objectives of Session: Attendees will learn 1) the process of identifying more precise and appropriate measurement variables when engaging in human-adjacent microbiome research, instead of using proxy factors, 2) how to include more resolution to factorial data during collection, and 3) examples of how to process complex social data during microbiome data analysis.
Format of talks: Three 30-min lecture-style talks will disambiguate proxy categorizations into more precise variables that consider social contexts, approach to course, lessons learned/challenges.
Format of breakout rooms: Each room creates a concept map which disambiguates a proxy category into specific variables, and discusses how to frame surrey questions or leverage existing data to obtain this information. Each room has a designated topic area (e.g. environmental restoration) to help audience members group by discipline or type of information they are looking for.
“Proposal of Neighborhood Socioeconomic Status Based Analysis of Human Microbiome Project”
Dr. Katherine Maki, PhD., Assistant Clinical Investigator, Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center
Dr. Nicole M. Farmer, M.D., Principal Investigator, Translational Biobehavioral and Health Disparities Branch, NIH Clinical Center
Dr. Kelly K. Jones, Ph.D., RN, Research Fellow, Neighborhoods and Health Lab, Division of Intramural Research, National Institutes of Health
Dr. Osama Tanous, M.D., Palestinian pediatrician based in Haifa and a board member of Physicians for Human Rights – Israel; Visiting Scientist, FXB Center for Health and Human Rights, Harvard University; Hubert H. Humphrey Fellow of Public Health and Health Policies, Emory University. His recent publication can be found here.
“From bedside to the journal – understanding bacteria in a settler colonial setting”
12:30 – 14:15 Introduction and Speakers
14:15 – 14:30 Break
14:30 – 16:00 Breakout room discussions based on skills development, in smaller groups
Deconstructing race as a biological variable
Common pitfalls/challenges to experimental design
Matching clinical work to social contexts.
Bioethnography to generate hypotheses
Planning for variables in microbiome and social research
Combining microbiome and social data analysis
Prior to this session, you may want to watch these recorded talks:
Microorganisms are critical to many aspects of biological life, including human health. The collective microbial community, our microbiome, can be impacted by the details of our lifestyle, including diet, hygiene, health status, and more, but many are driven by social, economic, medical, or political constraints that restrict available choices that may impact our health. Access to resources is the basis for creating and resolving social equity, access to healthcare, healthy foods, a suitable living environment, and to beneficial microorganisms, but also access to personal and occupational protection to avoid exposure to infectious disease. This special session explores the way that microbes connect public policy, social disparities, and human health, as well as the ongoing research, education, policy, and innovation in this field.
Upon completion of this Cross-Track Symposium, the participant should be able to:
Recognize the connections that microbiomes have to social equity. This will be demonstrated with examples/case studies presented by speakers.
Discuss relevant issues in microbiomes and their connection to social equity and identify issues which could be explored further.
Appraise your own work for these connections between microbiomes and social equity, to designate places for professional growth and applying equitable design.
After this session, MSE will be having an informal meet up, as most of us have never met in person!
Presentations and posters from some of our Microbes and Social Equity group members
Please note, the presenters’ names are bolded, and this is not to denote which author is part of MSE. We have included these in order to cross-promote talks, but these presentations may be independent of members’ MSE activities. This is a non-exhaustive list.
Dispersal Limitation and Density-Dependent Processes Structure Streptomyces Populations at Small Spatial Scales.J. Hariharan, D. Buckley. Rapid Fire. S107. Rapid Fire: Ecology, Evolution, and Biodiversity. June 11, 2022, 8:15 – 9:05 AM. Lounge and Learn 2.
Microbes and Social Equity: what is it and how do we do it?. S. Ishaq. Session AES018 – Field Work & DEI: Fostering Equitable Partnerships with the Communities in Your Field. June 11, 2022, 11:45 AM – 12:30 PM. AES Track Hub, located in the Exhibit Hall.
Antibiotic Resistance at the Human-Animal Interface in Southeast Asia. M. Nadimpalli, M. Stegger, R. Viau, V. Yith, A. de Lauzanne, N. Sem, L. Borand, B-t. Huynh, S. Brisse, V. Passet, S. Overballe-Petersen, M. Aziz, M. Gouali, J. Jacobs, T. Phe, B. Hungate, V. Leshyk, A. J. Pickering, F. Gravey, C. M. Liu, T. J. Johnson, S. Le Hello, L. B. Price. SESSION Poster. EEB01 – Ecology of host-associated microbiomes. June 12, 2022, 10:00 AM – 4:00 PM. Exhibit and Poster Hall. Presenter available during Poster Presentation 1 (10:30 am – 12:30 pm).
The symposium will convene researchers from different disciplines, foci, and geographic locations, and fosters in-depth conversations and research skills development. It is an ideal venue for training graduate students and incubating their burgeoning ideas. Thus, students in the class will attend the symposium, engage in conversations before and after attending sessions to reflect on how our perspectives changed, and create written assignments that will receive peer and instructor feedback. If the course is successful, I hope to add additional instructors and enrollment, we will expand the course and host it again each year we host the symposium.
The last paper to be generated from the large-scale, multi-year, collaborative research I participated in as a postdoc at Montana State University in the Menalled Lab in 2016 has finally been accepted for publication! At the time, I was working on the soil bacteria associated with winter wheat crops under different simulated climate change scenarios, and with added stressors like weed competition and different farming strategies. I was part of a large team of researchers looking at various aspects of agricultural stressors on long-term food production, including several agroecologists who led the development of this paper.
Understanding the impact of biological and environmental stressors on cropping systems is essential to secure the long-term sustainability of agricultural production in the face of unprecedented climatic conditions. This study evaluated the effect of increased soil temperature and reduced moisture across three contrasting cropping systems: a no-till chemically managed system, a tilled organic system, and an organic system that used grazing to reduce tillage intensity. Results showed that while cropping system characteristics represent a major driver in structuring weed communities, the short-term impact of changes in temperature and moisture conditions appear to be more subtle. Weed community responses to temperature and moisture manipulations differed across variables: while biomass, species richness, and Simpson’s diversity estimates were not affected by temperature and moisture conditions, we observed a minor but significant shift in weed community composition. Higher weed biomass was recorded in the grazed/reduced-till organic system compared with the tilled-organic and no-till chemically managed systems. Weed communities in the two organic systems were more diverse than in the no-till conventional system, but an increased abundance in perennial species such as Cirsium arvense and Taraxacum officinale in the grazed/reduced-till organic system could hinder the adoption of integrated crop-livestock production tactics. Species composition of the no-till conventional weed communities showed low species richness and diversity, and was encompassed in the grazed/reduced-till organic communities. The weed communities of the no-till conventional and grazed/reduced-till organic systems were distinct from the tilled organic community, underscoring the effect that tillage has on the assembly of weed communities. Results highlight the importance of understanding the ecological mechanisms structuring weed communities, and integrating multiple tactics to reduce off-farm inputs while managing weeds.
The spring semester has brought quite a few changes to the Ishaq lab, including new members and graduating several seniors, new projects, new papers, and a multitude of events for the Microbes and Social Equity Working group!
We welcomed several new lab members to the Team, including Dorien Baudewyns (Husson, B.S. 2021), Louisa Colucci (Husson, expected graduation 2022), and Omar Tavio (freelance), who are all helping with master’s student Johanna Holman’s project on the gut microbiome in response to broccoli. In January, we were joined by Joe Balkan (Tufts University undergraduate student), who learned anaerobic culturing and assisted with the massive sample collection and processing initiative that followed the mouse experiment over the winter. Joe will be joining us again this summer as we continue that work with more anaerobic culturing and biochemical testing.
We welcomed Rebecca French, who is joining a collaborative team of undergraduate and faculty researchers at UMaine in the Orono and Presque Isle campuses. This pilot study will examine zoonotic diseases in some rodent species in Maine, and how climate change might be affecting their geographic locations and pushing them further north, thereby bringing certain pathogenic microbes to new locations or putting them in closer contact with people or livestock. Rebecca was awarded a 2021 J. Franklin Witter Undergraduate Research Endowment Fund award to support her research, which she will complete for her senior Capstone Experience in animal and veterinary studies. She’ll be joined by undergraduates in the Kamath and Levesque labs at UMaine, and eventually by an undergraduate in the Johnston Lab at UMPI.
We are also saying goodbye to some of our seniors, including Emily Pierce, the very first undergrad in the Ishaq Lab, who is headed for Kansas State University College of Veterinary Medicine to pursue her dream of becoming a veterinarian. Emily was awarded a 2021 CUGR Fellowship for her Capstone Experience research on Cryptosporidium parvum infection, for which she presented at the UMaine Student Symposium in April.
Jade Chin, also an undergraduate researcher, is heading to Glasgow University for her senior year after which she will attend as a veterinary student there. Jade completed a literature review of leaf silage as livestock feed for her UMaine Undergraduate Honor’s Thesis, which was successfully defended in May and awarded High Honors!
A collaborative paper on bacterial transfer in insects and the possible ecological impacts of that in the wild has been accepted for publication in iScience! This work began a decade ago in the labs of Dr. Ellie Groden, recently retired Professor of Entomology at the University of Maine, and later Dr. Patricia Stock, Professor of Entomology at the University of Arizona, who were investigating colony collapse of European fire ants (Myrmica rubra) which are invasive to Maine. The ants have a nasty bite, and can dramatically disturb the local plant and insect wildlife in coastal Maine. Most of the work for this project was completed several years ago, with the exception of DNA sequencing data from an bacterial transfer experiment. I was added to the project by my collaborator at UMaine, Dr. Jean MacRae, who introduced me to the research team and shared the16S rRNA dataset to use in my AVS 590 data analysis class in spring 2020. That semester was when the pandemic hit, and forced the course to move to remote-only instruction in March. UMaine graduate students Alice Hotopp and Sam Silverbrand were taking the class and learning 16S analysis on this dataset, and I mentored them through the analysis all the way to manuscript writing despite the incredible challenges that spring threw our way.
Another paper was accepted for publication, in Animal, using data analysis from the spring 2020 AVS 590 class, on the effect of a dietary additive on the rumen and fecal bacterial communities in dairy cattle! Similarly, the original experiment for this work took place several years ago, and involved an animal feeding trial which added reduced-fat distillers’ grains with solubles into dairy cattle feed. The research team found no negatives effect on milk production or animal health, and that work was previously published. To add to that project, the original research team wanted to know if the diet would drastically change the bacterial community living in the rumen, which would have implications for feed digestion and animal health. A collaborator of mine donated the cow microbial community DNA data to my AVS 590 special topics in DNA Sequencing Data Analysis course in spring 2020 (now formally registered as AVS 454/554). I worked with UMaine graduate students Adwoa Dankwa and Usha Humagain over the semester to train them in coding and develop the manuscript. The diet only had minimal effects on the bacterial community profiles, which in this case is a good finding – we want to be able to feed a cheap, nutritional source like distillers’ grains without harming the cow or its microbes.
Microbes and Social Equity
The Microbes and Social Equity Working Group had an extremely productive spring, including growing to more than 80 members internationally, hosting a 12-session speaker series which can be viewed here, organizing a virtual symposium for June, and organizing a journal special collection in partnership with a scientific journal. The special collection will highlight recent work, and review previous efforts in this field from a set of invited international authors, and which includes an Introduction to the ‘Microbes and Social Equity Working Group’ perspective piece featuring 35 members as authors.
This summer, in addition to the ongoing work mentioned above, I’ll be mentoring a student through the UMaine Research Experience for Undergraduates (REU) program. Myra Arshad is an undergraduate at Stony Brook University, in New York, and will be joining the lab remotely over the summer to participate in research and related professional development. Myra will be learning some data analysis to work on camel rumen samples as part of an ongoing collaboration with a researcher in Egypt, Dr. Alaa Rabee, as well as helping with the Microbes and Social Equity Working Group initiatives. Patrick Fludgate, a rising senior in Animal and Veterinary Sciences at UMaine, will be joining the project, as well, as he completes his senior project for the Capstone Research Experience.
The Microbes and Social Equity Working Group will be hosting a virtual symposium June 14 – 18, along with the UMaine Institute of Medicine. Over 5 sessions, we will explore how microbial exposure can affect human and ecosystem health, and discuss research, education, and policy which can promote equitable access to beneficial microbes. Registration is free.
Finally, the Ishaq Lab and affiliates will be presenting some research at conferences this summer:
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). ASM Microbe/ISME World Microbe Forum 2021 (virtual). June 20-24, 2021.
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)
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)
Fall 2020 is the beginning of my second year as an assistant professor at the University of Maine, but in some aspects, it feels like my first year.
The most prominent visual which evokes this feeling is the new office I just moved into last week. My new office space overlooks my two renovated lab spaces and allows me to witness the first official Ishaq Lab research take shape. My first office was in a building across the street from the two labs, all of which I was inheriting from a previous lab. This reduced our output for several reasons, in particular because undergraduates could not access or be left alone in the lab early on in their training. For several months, when students were in the lab, I was there, too, trying to maintain productivity while on my laptop. And, I needed to be present for several deliveries, meaning I would have to wait around. For the better part of the last year, several students and I have redesigned the space to fit our needs, and it was only over this summer that the microbiology space finally was sorted. Now, I can be close by to answer questions, sign for packages, and sort out problems.
Not only do I have spaces ready for my research, but this year I am also starting with students to perform it. It takes time to recruit students to your lab, and graduate students take particularly long because of application submission or funding start dates. Over the past year, I have been joined by two thesis master’s students, one non-thesis master’s student, 3 graduate students from other labs who do collaborative work with mine, 6 undergraduate researchers, and a handful more partial time undergraduate researchers through the Animal Science Capstone class (more on that further on). The projects range from gut microbes and health, soil microbes in blueberry fields, the use of leaves for home silage, lobster microbes and water temperature, and more! The team is dynamic, curious, and a delight to work with.
To ensure that we stay safe, we manage our lab occupancy with a shared lab calendar (and several of the students are performing partial or fully-online projects). Both spaces are designated for Biosafety Level II work, which means we are already wiping down surfaces with disinfectant before and after use, wearing gloves and a lab coat, and washing our hands before and after work. The air exchange systems stay on to prevent moisture or fume buildup, and they also remove particles from the air, but I have added HEPA filtration units in each lab and my office to remove additional particles (including viruses) from the air. A robotic vacuum in each space cleans dust and settled microbes off the floor each night. In addition, we now limit occupancy, wear masks when multiple people are in the room, and check in/out of the space to facilitate contact tracing.
This semester also feels like my first because I am teaching official courses for the first time. Between the two courses, I am teaching over 50 students! I expect that to increase next fall as my new course becomes more well-known, and as recruitment and retention continue to rise in Animal and Veterinary Studies.
I’m also teaching one on undergraduate research which is a long-standing class that I generated some new materials for. I will teach part of this each fall, and part each spring. Over the academic year they participate in research, then write proposals and reports.
Students generated a word cloud of descriptors for ‘scientist’. At the end, we’ll make a new cloud to see if their impressions change after participating in science.
Over the fall, I have a number of research projects to wrap up from the spring, such as data analysis projects which arose from my DNA sequencing data analysis course, one of which on ants I was invited to present at the virtual Entomological Society of America scientific conference in November! I’m also wrapping up a few small projects which originated over the summer, such as the blueberry soil pilot or the lobster microbes data analysis performed by my REU student-turned-direct-hire. I’ll also be starting several new projects on the interaction between gut microbes and the host, led by my graduate students and a number of undergraduates, which will form the core of the research in our lab.
In addition, my Microbes and Social Equity working group is gaining traction! At over 40 participants, the MSE group has been met with interest and enthusiasm from different research and professional fields, and levels of career stage. We are planning to collaborate on a journal special collection, as well as organize a mini meeting sometime in 2021. I look forward to bringing attention to important and timely work on microbes, health, and public policy!