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:
Not only is the ongoing ‘COVID-19’ pandemic a collective experience and historical event, it has changed the way we interact with each other and with our infrastructure. It’s pertinent to incorporate these events into teaching curricula, not only to study these changes in real time, but to help us make sense of what is happening during these difficult days. A number of faculty at the University of Maine have been and will be integrating various aspects of the pandemic into their teaching. For my part, I’ll be guiding students on research projects related to how COVID-19 and public policy has affected agriculture and veterinary practice.
“COVID has very suddenly and dramatically changed the way we interact with each other, and has had repercussions for food, agriculture and animal care industries,” Ishaq says. “Students need to understand these changes to build more resilient and sustainable food and health care systems.”
“Faculty incorporate COVID-19 content into curricula”, Marcus Wolf, June 23, 2020
As a new assistant professor at the University of Maine, 50% of my appointment is research. To establish my research, I started with curating a space to fulfill the needs of my work — “professional nesting”, if you will. I was allotted two adjacent rooms for my lab work, one as a microbial culturing space, and one for genomics work. I asked for and was granted separate spaces to reduce to likelihood of contamination sourced from my culturing space.
Prior to my arrival at the University of Maine, both lab spaces were set up to perform different research from what I do. This may not seem like it would interfere with my work, but the type of research you do will influence the machinery you need, each of which may have space or utilities requirements, as well as the flow of traffic through the room. To reduce the amount of time you spend moving around the room in search of elusive supplies, it’s best to curate work stations within the room. To that end, the Ishaq lab team spent several days re-arranging the large machinery and the table-top equipment, and then moving the supplies to the cabinets in corresponding locations. This change was most evident in the genomics room, that was previously used for human cell culture and biochemistry, shown below. At this time, I’m still working on updating the microbial culture room, which is larger and contained many more bits and pieces to organize.
Most research labs use extremely specialized equipment and machinery. Some of this was made available to me immediately; when research labs are discontinued, ownership of equipment and consumable materials reverts back to the researcher’s home department. I needed to purchase some of the more research-specific equipment, using some of the funds allotted to me for this purpose. Buying equipment can be stressful, because it can be incredibly expensive, and you want to be sure you selected the machine brand and range of capabilities for what you might want to do over the next 5 – 10 years, at least.
Finally, you need to stock your lab with reagents and researchers, but both of these have been temporarily put on hold as of March 2020, as we do our part to reduce the transmission of the Covid-19 virus. Whenever it is safe to do so, I look forward to completing the updates to my spaces and opening them up for collaborative work.
I’m pleased to announce that a small grant proposal I am part of was just funded by the Northeastern Integrated Pest Management (IPM) Center! The proposal, “A Working Group on Tarping and Soil Solarization”, brings together researchers and food production professionals from across New England to identify the current use of tarping and soil solarization to prevent weed growth without the use of chemcials, as well as identify barriers to adoption of this practice, and develop research proposals to fill any knowledge gaps related to the use of these methods and their effect on crop production, weed suppression, soil microbiota, and the local ecosystem.
Led by Dr. Sonja Birthisel (UM), the working group team is comprised of Dr. Alicyn Smart (UM), myself, Master Nathalie Lounsbury (UNH), and Eva Kinnebrew (UVM). We will be joined by over a dozen other researchers across New England who perform agricultural research, along with dozens of ‘stakeholders’: producers and other food production professionals who have an interest in the group findings and would make use of any knowledge we generate.
Now that I’m an assistant professor, a significant amount of my time is spent writing grant proposals to fund projects I’d like to do in the future.
Many large federal or foundational grants take up to a year from submission to funds distribution, and the success rate, especially for newly-established researches, can be quite low. It’s prudent to start writing well in advance of the due date, and to start small, with “pilot projects”.
To that end, I’m pleased to announce that Dr. Lily Calderwood and I just received word that the Wild Blueberry Commission of Maine is funding a pilot project of ours; “Exploration of Soil Microbiota in Wild Blueberry Soils“. We’ll be recruiting 1 – 2 UMaine students for summer/fall 2020 to participate in the research for their Capstone senior research projects.
Dr. Calderwood is an Extension Wild Blueberry Specialist, and Assistant Professor of Horticulture in the School of Food and Agriculture at UMaine. She and I developed this project when meeting for the first time, over coffee. We realized we’d both been at the University of Vermont doing our PhD’s concurrently, and in neighboring buildings! We got to chatting about my work in wheat soil microbial communities, and her work on blueberry production, and the untapped research potential between the two.
This pilot will generate some preliminary data to help us get a first look at the soil microbiota associated with blueberries, and in response to management practices and environmental conditions. From this seed funding, Lily and I hope to cultivate fruitful research projects for years to come!
My first official course at the University of Maine has been approved! Starting Fall 2020, I will teach AVS 254: Introduction to Animal Microbiomes!
This 3-credit course is geared towards undergraduates with a science background, with sophomore status or higher. Some familiarity with microbiology, genetics, mammalian anatomy, or microbial ecology would be helpful, but is not specifically required.
The working syllabus can be found here, with more information on lectures, assignments, workload, classroom policies, and more:
Description: This course introduces students to host-associated microbiomes; the genomic collection of bacteria, archaea, fungi, protozoa, and viruses present in a host ecosystem. In each lecture, we will focus on an anatomical location, and discuss the host and environmental pressures which select for the resident microbial community. The material is primarily in animals (mammals, birds, fish, amphibians) but includes some human-specific comparisons. This course will introduce ecological theories (e.g. environmental selection, neutral theory) in the context of microbial communities, the history of host-associated microbiology, and how technology has contributed to or limited our understanding of organisms and their critical role in our health and development. The skill-set objectives include group discussions, reading scientific literature, and scientific writing in a variety of styles and both technical and non-technical formats.
I’ll be returning to the field I started in; gut microbiology, but I’ll be integrating things I picked up along the way over the past few years, including ongoing collaborations in soil and built environment microbiology. I’ll be right at home in the UMaine School of Food and Agriculture, which brings together animal science, nutrition, and plant and soil science.
In addition to formally starting my own lab, I’m looking forward to snowy winters and summers on the rivers.