Emily joined the lab in early 2020 to work on a project investigating calf health and gut microbes, but very soon after joining the lab, the SARS-CoV-2 pandemic emerged and changed the way we were able to interact on campus. Without missing a beat, Emily shifted her efforts from helping me wrangle the lab renovations and sorting out our inventory, to helping me improve my teaching materials, to diving deep into previous literature to dig up protocols for her experiment in 2021: “Ideal Conditions for Cryptosporidium Attachment and Infection.“
We’ll be performing the experiment itself over the winter break, and then using the spring to analyze the data and write them up. As part of the CUGR award, Emily will be presenting her work at the 2021 Student Symposium in April, which will be held virtually this year. You’ll have to wait till then to get more details!
With the closing of the fall semester, I said goodbye to the students in my AVS 254: Introduction to Animal Microbiomes class. Despite the challenges and turmoil of fall 2020, these students have been engaged, enthusiastic, and creative. After presenting lectures on the microbial communities in and on animal hosts and how they can impact health and fitness, for the final class of the semester, I wanted to close with perspectives from the broader world of science.
To that end, I compiled several videos of “science journeys”, as told by active researchers in host microbiology, with an introduction to the class/video and my own science journey. I hope to compile a new volume each year I teach the class, to gather diverse paths.
I am extremely grateful for the time, effort, and thoughtfulness of the researchers who were able to contribute during a hectic semester to volume one:
Edna Chiang, University of Wisconsin Madison, @EdnaChiang
Dr. Kaitlin Flynn, Benaroya Research Institute in Seattle, @microkaitlin
Kiran Gurung, University of Groningen, @kirangurung29
Jocelyn R. Holt, Texas A&M University, @JocelynRHolt
Chissa Rivaldi, University of Notre Dame, @Powerofcheez
Dr. Laura Tipton, Chaminade University of Honolulu, @lauraomics
Dr. Benjamin Wenner, The Ohio State University, @Bynjammin
Mice have arrived for a collaborative project on diet, gut microbes, and health in conjunction with researchers at Husson University! This is the first mouse project for the Ishaq Lab, and also my first hands-on mouse project (in my previous publications with mice, I received datasets but the mouse work was performed solely by my collaborators).
This is one of my first new collaborations at the University of Maine, which began in September 2019 as I was just finding my way around campus. An established researcher at Husson University, Dr. Yanyan Li, reached out to welcome me and talk about overlap between our work. Yanyan, her husband Dr. Tao Zhang, also a researcher at Husson University, and collaborator Dr. Grace Chen at Michigan State University, had been working on beneficial compounds found in broccoli using mice as an experimental model for Inflammatory Bowel Disease (IBD). Over the past year, in consultation with IBD experts Drs. Gary Mawe and Peter Moses (who I worked with previously while at UVM!), we have written several proposals for funding to expand the project.
Johanna Holman worked for several years with Yanyan and Tao, as an undergraduate researcher and then as a research assistant. She joined the Ishaq Lab this fall to continue her work as a graduate student and add gut microbiology to her skill repertoire. This experiment will form the base of her graduate thesis, and Johanna is taking a lead role in managing the project as well as several undergraduate researchers, including Dorien Baudewyns, assisting with the mice and lab work. As an early career researcher, and new to mice, I’m extremely lucky to be able to learn from an experienced team of researchers!
2020 has been an interesting year for scientific conferences and meetings, which typically bring dozens to thousands of researchers and professionals together to share their work. Some of the bigger meetings, or those occurring early on in the pandemic, elected to cancel their events because there was no time to adjust the logistics for hosting a massive meeting online.
As the year progressed with no sign of the pandemic abating, more conferences opted for a modified event online. This included live-stream and/or recorded content, spacing the event over a longer period to reduce “zoom fatigue”, and making network events smaller virtual versions. It certainly would have been more rewarding to be able to have these in person, but I am pleased that conference organizers chose safety as their priority.
In some ways, having virtual content made the material more accessible. recordings meant you could watch content at your convenience, more organizations provided or required subtitles for presentations, and those who would otherwise not be able to attend, because of cost, childcare, or travel constraints, were able to participate.
The Ishaq Lab presentations for 2020 is below, with presenters denoted with an asterisk (*).
Ishaq*, S.L.”Framing the discussion of microorganisms as a facet of social equity in human health”, inVIVO Planetary Health 2020 meeting. (revised to virtual) Amsterdam, Netherlands. Dec 2020.
Yeoman*, C., Lachman, M., Ishaq, S., Olivo, S., Swartz, J., Herrygers, M., Berarddinelli, J. “Development of Climactic Oral and Rectal Microbiomes Corresponds to Peak Immunoglobin Titers in Lambs.” Conference of Research Workers in Animal Diseases (CRWAD) 2020. (revised to virtual) Dec 5, 2020.
Ishaq*, S.L., Hotopp, A., Silverbrand, S., MacRae, J., Stock, S.P., Groden, E. “Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?” Entomological Society of America 2020. (revised to virtual). Nov 15-25, 2020.
Menalled*, F.D., Seipel, T., Ishaq, S.L. “Agroecosystem resilience is modified by management system via plant–soil feedbacks.” Ecological Society of America (ESA) 2020. (revised to virtual) Salt Lake City, UT. Aug 2020.
[meeting cancelled] Horve*, P.F., Dietz, L., Ishaq, S.L., Fretz, M., Van Den Wymelenberg, K. “Characterization of Viable Microbial Communities on Healthcare Associated Window Components.” American Society for Microbiology Microbe 2020, Chicago, IL. Jun 2020.
[meeting cancelled] Horve*, P.F., Dietz, L., Ishaq, S.L., Fretz, M., Van Den Wymelenberg, K. “Characterization of Viable Microbial Communities on Healthcare Associated Window Components.” 2020 Microbiology of the Built Environment (MoBE) Gordon Research Conference, Andover, NH. Jun 2020.
Zeng*, H., Safratowich, B.D., Liu, Z., Bukowski, M.R., Ishaq, S.L. “Supplementation of calcium and vitamin D reduces colonic inflammation and beta-catenin signaling in C57BL/6 mice fed a western diet.” American Society for Nutrition 2020. (revised to virtual) Seattle, WA. June 2020.
Last Friday, I gave a seminar on “A crash course in the gut microbiome” to the University of Maine Institute of Medicine as part of their fall seminar series. You can find the previous seminars in that series here.
I was delighted to have the opportunity to share my science to researchers around Maine, and to have so many engaging questions!
You can find my seminar recording here, and a pdf of the slides with my presenter notes as annotated comments can be found here:
This fall, my speaking engagements will all be held virtually, to aid in ongoing infectious-disease-prevention protocols. While in place to reduce the spread of SARS-CoV-2, these same protocols will also help me avoid the annual fall respiratory infection that I otherwise inevitably encounter while working with overly-stressed students.
But, staying away from others doesn’t mean I can’t stay connected! Virtual events might not feel as fun, but they have allowed me to reach a wider audience, because recorded talks are made available after the live event. And, annotated or subtitled recordings make my talks more accessible!
This fall, I have several public talks and scientific presentations lined up:
University of Maine Cooperative Extension Oxford County 4-H Teen Science Cafe (virtual), “Gut microbes on the farm”, Oct 15, 2020. For teens, this event is free but does require registration to obtain the link.
Genomes to Phenomes (G2P) group, University of Maine. Co-hosting a session with grad student Alice Hotopp, on gut microbes and survival of reintroduced animals. Oct 30, 2020. Link available to University of Maine community members.
University of Maine Medicine seminar series (virtual), “A crash course in the gut microbiome” , Nov 6, 2020. This event is open to the public and free, but does require registration to obtain the link.
Hotopp, A., Silverbrand, S., Ishaq, S.L., MacRae, J., Stock, S.P., Groden, E. “Can a necromenic nematode serve as a biological Trojan horse for an invasive ant?” Entomological Society of America 2020 (virtual). Nov 15-18, 2020. This pre-recorded seminar requires paid event registration.
Yeoman (presenter), C., Lachman, M., Ishaq, S., Olivo, S., Swartz, J., Herrygers, M., Berarddinelli, J. “Development of Climactic Oral and Rectal Microbiomes Corresponds to Peak Immunoglobin Titers in Lambs.” Conference of Research Workers in Animal Diseases (CRWAD) 2020. (Virtual) Dec 5, 2020. This seminar requires paid event registration.
Almost ready for my "Microbes on the farm" presentation to the Oxford County 4H kids! And I finally had to chance to use this photo from my 2015 lamb study. pic.twitter.com/cq43EctXWZ
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.
Before (as a nutritional biochemistry lab) and after (as a microbiology lab). Anaerobic chamber is not in the photo frame.
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!
From their main page, you can find descriptions of each virtual session, including subject material, presenter, and recommended age group (k-12). You can register for as many or as few sessions as you like, which will be delivered over Zoom.
Registration is free! But if you are able to donate to support the program, those are welcome through the 4H site.
I’ll be presenting on Thursday, August 13th, 2020 at 3 pm EST.
Learn about different digestive tracts in livestock, and the community of microbes living there that help animals digest food, or stay healthy. This presentation will give some background on different digestive tract anatomy, the factors which influence microbes in the gut, and how we can care for animals by caring for their microbes. This presentation will also feature a short presentation on Dr. Ishaq’s journey into science and a Q&A session where attendees can ask questions about gut microbes, life as a scientist, or how to get involved in this time of career. Register by August 12.
In a 2019 collaboration between the Biology and the Built Environment Center at the University of Oregon and the Oregon Health & Sciences University, we sampled various window surfaces from patient rooms in a hospital ward. We characterized the viable bacterial community located on these surfaces, and investigated the association of relative light exposure of the surface (in direct light or not), the cardinal direction of the room (and roughly the amount of total light exposure in a day), and proximity of the patient room to the nurses’ station (which has higher occupancy and traffic).
Figure 1. Floor plan and rendering of a typical patient room at the Oregon Health and Science University hospital. (a) Floor plan of the 13th floor of Kohler Pavilion (13K) at Oregon Health and Science University (OHSU). Red shading indicates the rooms that were sampled between 10:00 a.m. and 11:00 a.m. on June 7, 2019 (b) Digital rendering of a typical patient room on OHSU (13K) with the sampling locations indicated by the numbers. The sampled locations were (1) window glass surface, (2) the window frame surface facing into the room at the sill, (3) glazing-side of the window frame at the sill, (4) window-side of the curtain, (5) patient-side of the curtain and, (6) wood-covered air return grille.
The microbial community found in buildings is primarily a reflection of the occupants, and in the case of hospitals, the microbiota may be sourced from patients, staff, or visitors. In addition to leaving microbiota behind, occupants may pick up microorganisms from building surfaces. Most of the time, this continuous exchange of microorganisms between a person and their surroundings is unremarkable and does not raise concerns. But in a hospital setting with immunocompromised patients, these microbial reservoirs may pose a risk. Window glass, sills, and the surfaces around windows are often forgotten during hospital disinfection protocols, and the microbial communities found there have not previously been examined.
This paper is the first first-authored research paper from a former undergraduate mentee of mine at the University of Oregon; Patrick Horve.
Horve, 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. Impact 2.353. Article.
I’m pleased to announce that an article was published today on soil microbes, climate change, and agriculture! As local climates continue to shift, the dynamics of above- and below-ground associated bio-diversity will also shift, which will impact food production and the need for more sustainable practices.
This publication is part of a series, from data collected from a long-term farming experiment in Bozeman, MT, led by researchers at Montana State University with whom I have published several times, including:
Weed communities and wheat yield are modified by cropping systems and climate conditions. In review.
In this study, cropping system (such as organic or conventional), soil temperature, soil moisture, the diversity and biomass of weed communities, and treatment with Wheat streak mosaic virus were compared as related to the bacterial community in the soil associated with wheat plant roots.
This paper is open-access, which means anyone can read the full paper.
Little knowledge exists on how soil bacteria in agricultural settings are impacted by management practices and environmental conditions under current and predicted climate scenarios. We assessed the impact of soil moisture, soil temperature, weed communities, and disease status on soil bacterial communities between three cropping systems: conventional no-till (CNT) utilizing synthetic pesticides and herbicides, 2) USDA-certified tilled organic (OT), and 3) USDA-certified organic with sheep grazing (OG). Sampling date within the growing season, and associated soil temperature and moisture, exerted the greatest effect on bacterial communities, followed by cropping system, Wheat streak mosaic virus (WSMV) infection status, and weed community. Soil temperature was negatively correlated with bacterial richness and evenness, while soil moisture was positively correlated with bacterial richness and evenness. Soil temperature and soil moisture independently altered soil bacterial community similarity between treatments. Inoculation of wheat with WSMV altered the associated soil bacteria, and there were interactions between disease status and cropping system, sampling date, and climate conditions, indicating the effect of multiple stressors on bacterial communities in soil. . In May and July, cropping system altered the effect of climate change on the bacterial community composition in hotter, and hotter and drier conditions as compared to ambient conditions, in samples not treated with WSMV. Overall, this study indicates that predicted climate modifications as well as biological stressors play a fundamental role in the impact of cropping systems on soil bacterial communities.
The Ishaq Lab 