I’m delighted to officially announce that the Ishaq Lab is welcoming two new graduate students this year, Johanna Holman and Sarah Hosler! Both of them will be working on dynamics of the gut microbiome, and starting a master’s of science this summer/fall. Johanna and Sarah are wonderful additions to our current, enthusiastic team, and the Ishaq Lab can’t wait to see what you achieve!
Johanna Holman
Fall 2020 Masters of Science, Human Nutrition and Food Sciences
Johanna is joining the lab in Fall 2020 to investigate the effects of diet on the gut microbiome, and on host-microbial interactions.
Sarah Hosler
Fall 2020 Masters of Science, Animal Science
Sarah is from Newton, NJ and has lived in NJ her whole life until she started college at Albright College in PN. Her undergraduate research was on protein classification. Sarah is joining the lab in Fall 2020 to create new methods for studying host-microbial interactions.
“I am excited to see how much I grow through my graduate experience at the University of Maine. I’m also a little bit nervous about the cold, but I’m sure I will get used to it.”
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!
One of the biggest challenges faced by STEMM (science, technology, engineering, math, medicine) advocacy groups is finding the time and resources to propose and execute initiatives, as well as find the time for social media engagement to grow the group. There are a number of groups already established in Maine which seek to promote STEMM advocacy/education, accessibility, diversity/equity/inclusion, campus community members, and the general public.
STEMMinists of Maine is a newly-formed STEMM advocacy group, which seeks to bring together these various groups. Our goal is to act as an umbrella organization, to create a cohesive social media presence that makes it easier for people interested in STEMM advocacy and inclusion to find resources, coordinate events, and get the message out. All participating groups will remain autonomous, but participation (which is free) will hopefully allow us all to reach a broader audience and have a greater impact in both campus and state-wide initiatives.
Our inaugural meeting will be held at the University of Maine campus, 57 Stodder Hall, to introduce STEMMinists and invite others to be part of our work to promote a better STEMM community. All are welcome!
Shortly after, our website and social media will be finalized and launched!
The Ishaq lab has been quietly growing, and we had our first official meeting today! I can’t wait to see what we accomplish together.
We are all such rock stars, we needed to meet virtually to keep up with our busy schedules!
Top left: Adwoa, a PhD student in Dr. Jen Perry’s lab, working on kombucha microbes. Top right: in the office with me, Alexandria, an MPS student working on research techniques for gut microbes. Bottom left: senior member Tindall, a MS student at Montana State University in the Menalled/Seipel lab working on soil microbes. Bottom left: Johanna, incoming MS student in nutrition who will be working on diet and gut microbes. Undergrad Emily couldn’t make it, and we have a few more pending members and affiliates joining us in 2020.
I’m pleased to announce that I have been elected the Pod Coordinator for the Orono Pod of 500 Women Scientists! This spring, I hope to expand membership in and around Orono, connect with other inclusion and STEMM groups in Maine, and roll out some new initiatives and public engagement events.
500 Women Scientists is a non-profit, grassroots organization started by four women. Immediately following the November 2016 election, they published an open letter re-affirming their commitment to speak up for science and for all genders, minorities, immigrants, people with disabilities, and LGBTQIA. This commitment became a global movement, and that movement has blossomed into a formal organization dedicated to improving science communities. As of January 2018, 500 Women Scientists has over 20,000 members and supporters.
Building communities and fostering real change comes from small groups, not large crowds. Ourlocal podshelp create those deep roots through strong, personal relationships. Pods focus on issues that resonate in their communities, rooted in our mission and values. As women in science, technology, engineering and math, as role models to young girls and women, as leaders in our communities, we accept this challenge. Accept this challenge with us.
I was previously a Pod Coordinator in Eugene, where I coordinated group networking and public engagement events with a fabulous group. I’m looking forward to developing the same heartfelt connections here.
The journal is called Frontier for Young Minds, and pairs a young scientist with an established scientist to review your articles, a ~1,500 word summary version. The journal provides cartoon illustrations that help bring your science to life.
Ours was written by an undergrad I was mentoring at UO, Sam Rosenberg, and architecture grad student Julia May helped us with our Figures. I wasn’t involved with the original article, but along with Ashkaan, I helped Sam draft the summary as non-technical summaries of highly-technical science can be a real challenge. Check it out!
Rosenberg, S., Ishaq, S., May, J., Fahimipour, A.K. 2020. How light exposure changes bacterial communities in household dust. Frontiers for Young Minds.Article.
Notwithstanding the different reasons, 2019 has left us reeling, myself included. Early in the year, I was left scrambling to keep my science career going in the face of unsteady funding resources. Through a combination of collaboration, long hours of writing, a strong support network, a lot of luck, and a pragmatic demeanor, I landed a tenure-track faculty position and pulled off one of the best years of my career, to date. I deeply appreciate all of the concern, assistance, coffee, revisions in a timely manner, coffee, and support provided by so many individuals in the last year.
My momentous research activity of 2019 was joining the faculty of the University of Maine, Orono, School of Food and Agriculture as an Assistant Professor of Animal and Veterinary Sciences, beginning in September. In August, my partner, our patient dog, and I drove from the west coast to Maine on a 9-day adventure that would begin a new (and more permanent) phase of our life. From our education in Vermont, to my post-docs in Oregon, to my research faculty position in Oregon, to Maine, we loved the opportunity to live in various states, but are looking forward to having an address for longer than 2 years and more stable income forecasting.
We’ve driven over 7,000 miles in search of academic positions!
Leaving Oregon.
Arriving in Maine and Izzy can barely contain her enthusiasm.
The first few months of my faculty position have been busy! Notably, it’s involved a LOT of training, paperwork, getting acquainted with campus resources, and making connections. Some of these have involved seeking approval to take on graduate students, not just from my department, but students from other departmental programs that want their research to center around my lab’s specialties. UMaine strives to provide interdisciplinary opportunities for students, and as such, encourage multiple cooperating positions. In addition to being able to bring on grad students through the School of Food and Agriculture, I have just been approved as faculty in the Graduate School for Biomedical Sciences and Engineering, and have another cooperating position pending.
My work now spans three major research priorities. My lab will focus on the gut microbiome of livestock, and how microbes can be used to promote animal health and production. This will take shape in a variety of ways, including through global collaborations (more on those as they develop, but many of my previous rumen collaborations that began at Montana State are included in that). I’ll be taking on several graduate and undergraduate students in 2020 for these projects.
Through ongoing collaboration on projects led by Drs. Fabian Menalled and Tim Seipel at Montana State University, I’ll be participating in research to understand climate change and farming practices on wheat production and soil microbes. I am a graduate committee member for Tindall Ouverson, who is completing her master’s at MSU.
I’ll also be collaborating with researchers on microbes in the human gut. Through ongoing collaborations with researchers at the Institute for Health in the Built Environment (primarily those at BioBE) at the University of Oregon, I’ll be looking at infectious disease transmission and building design. And I’m currently developing new collaborations with researchers at Husson University, University of Maine, University of Vermont, and other institutions, which will investigate the interaction between diet, gut microbes, and human health. I’ll be taking on several graduate and undergraduate students in 2020 for these projects.
I published a record 10 papers this year! I don’t expect to achieve this again anytime soon: over the spring and summer I was only working half-time, and with the rest of my time I was doggedly writing up previous project results, overseeing undergraduate authors, and emailing co-authors for revisions. Writing or managing the writing of a manuscript takes a significant amount of work. Even when experiments or field trials are completed within days, weeks, or months, it may takes years to process, analyze, and measure the samples you collect, as well as complete the statistical analysis. You might encounter technical problems, or need to validate a method for use with your research. After all, much of what researchers do is trying new things, as there isn’t always a well-validated protocol to follow and you need to come up with something new. Thus, at least half of the publications from 2019 were wrapping up experiments that had occurred as far back as 2014!
Over the summer, I taught “Microbes and Social Equity” at The University of Oregon for the Clark Honors College. In just four weeks, the students, a few guest speakers, and I collectively wrote a paper to introduce the topic. We submitted it to the journal PloS Biology, and it was accepted for publication in their special call, Microbiomes Across Ecosystems. You can read it here. In the first month, it’s been viewed nearly 5,000 times!
I am developing new coursework for the University of Maine, including AVS 254 Introduction to Animal Microbiomes, which will be taught annually beginning in Fall 2020. This spring, I’ll be teaching a ‘special topics’ class, which will be the preliminary version of a class I am currently developing: DNA Sequence Data Analysis Lab, which will teach students the programming and analysis required to understand complex DNA sequence data, including amplicon, whole-genome, and metagenomics datasets. The special topics version is limited enrollment, and a way to beta-test the class before spending the significant amount of time required to develop a new course. I’ll be sharing more info about the classes as they develop.
Consortium meeting in Portland, OR. It was a quiet summer for me, but I did attend the Gordon Research Conference on Animal-Microbe Symbioses in Vermont, which showcased fascinating research on the ways that humans and animals interact with the microbes that inhabit our bodies. In October, I had a whirlwind week-long trip which involved giving a presentation in Monterrey, Mexico, then a different presentation in Reno, NV the following day, then heading to Bozeman, MT to catch up with collaborators and teach bioinformatics to Tindall. All of the meetings, seminars, and training was very valuable, but the best part, hands-down, was going to Matacanes canyon.
Rappelling down through a waterfall into a cave.
Outreach
Over 2019, I gave more than ten (not all have been published) interviews on my research! This included a live radio interview, and two podcasts: all new experiences for me.
I published 30 posts this year, including this one, although with ~11,000 words total, I had less to talk about. I anticipate that will change when my lab gets rolling. The most popular post this year continues to be Work-Life Balance: What Do Professors Do?, self explanatory, and the least popular this year is I Accepted a New Position in Soil Microbiology and Agroeconomy!, which makes sense as it was an announcement from 2016 about a post-doc position I’d accepted.
My site had its most popular year, with >4,000 visitors taking >6,000 views, represented by 109 countries. In total, my site has had > 10,000 visitors and >15,000 views since Jan 2016
Website visitors in 2019.
Life
If you’ve read this far, you can probably guess how hectic my life has been this year. At the same time, it’s been gorgeously complex. I finally made it down to see Crater Lake in Oregon, went powder skiing in the Rockies in Utah, drove through the dramatic beauty of the Rockies in Alberta, made my first visit to Mexico and was immersed in the isolated beauty of a mountain canyon in Matacanes.
This Year in Review, I have the clearest idea of where my 2020 is heading. With a new lab and new classes, I’ll be happily well-occupied. I’ll be obtaining 3+ quotes to buy each piece of lab equipment (if it cost more that $6,000) and then waiting two months for it to arrive, troubleshooting R problems and revising scientific manuscripts written by first-time authors, I’ll be training my new brood of students in the lab, and I’ll be sharing my experiences here! Stay tuned!
I have joined the graduate faculty in the Graduate School of Biomedical Science and Engineering (GSBSE) at the University of Maine. GSBSE is an interdisciplinary graduate program which spans not only multiple graduate programs at UM, but at four other institutions in the state. As faculty in the program, I can now accept graduate students whose research doesn’t fit under the umbrella of one specific field.
The Ishaq Lab 
