Spring 2021 in review

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!

Research Team

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.

Johanna won a 2020-2021 University of Maine Graduate Student Employee of the Year! Over the 20/21 academic year, Johanna was a Graduate Teaching Assistant for the Chemistry department, in addition to taking classes and managing a large research project.

Undergraduate researcher Nick Hershbine: 2020-2021 University of Maine Undergraduate Student Employee of the Year! Nick has been working on soil from blueberry fields in Maine.

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.

Summer Outlook

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:

  1. 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.
  2. 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)
  3. 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)
  4. The Microbes and Social Equity Working group, “Special Session 17: “Microbiomes and Social Equity” (19205).”, Ecological Society of America 2021. (virtual). Aug 5, 2021.
  5. Choi*, O.N., Corl, A., Wolfenden, A., Lublin, A., Ishaq, S.L., Turjeman, S., Getz, W.M., Nathan, R., Bowie, R.C.K., Kamath, P.L. “High-throughput sequencing for examining Salmonella prevalence and pathogen -microbiota relationships in barn swallows.”  69th Annual – 14th Biennial Joint Conference of the Wildlife Disease Association & European Wildlife Disease Association (virtual) Aug 31 – Sept 2, 2021. 

A branch of bright red maple leaves with green maple leaves further up the branch. The background is blurred, but shows a forest under an overcast grey sky.

Fall 2020 outlook: new students, new courses, new circumstances

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 developed one of my own design on animal microbiomes, and you can follow my tweets about the class under #animalmicrobiomes @drsueishaq

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!

DNA double helix with dollar signs as a nucleotide.

Extrava-grant-za!

Today a large-scale federal grant proposal was submitted, bringing me to four proposals submitted so far in 2020 (and eight total in the 2019/2020 academic year)! I have one more that is planned for the end of May, and two more that may be submitted this summer depending on the disposition of my pending proposals. Each of these proposals takes weeks to months of planning, writing, and coordination between the research team. The proposal submitted today was 107 pages, and only some of those materials can be re-used between grants, such as descriptions of equipment and research facilities.

A stack of papers facedown on a table.
So. many. supporting documents.

The success rate for obtaining federal funding for your project varies by agency, year, and category of project/principal investigator, nicely tracked here (updated Dec 2019), and currently ranges from 8 – 30%. For example, “pilot” project (small projects to “seed” your long-term research), student-specific, or “new investigator” grants may have a higher rate of success because their applicant pool is restricted by eligibility. Competition is fierce, especially when federal agency budgets are cut or re appropriated.

If projects are not funded, they are returned with reviews from typically 2 – 4 experts in the field who provide comments and recommendations for strengthening the experimental design, or the presentation of the project itself. You might think that proposals are judged on the merit of the science alone, but the ability of the team to manage the project, and the research team, is also being evaluated. Principal investigators (researchers like me, leading the project) need to show that we have good ideas and the organizational skills to implement them, especially if the project spans multiple years or institutions.

Submitting a research proposal is worth celebrating – it represents weeks of effort – but especially during this time when we are all trying to keep our head above water, never mind accelerate or productivity. It’s important to take a few minutes to relax, work can wait, because ‘the grind’ will be there waiting for you when you get back.

Picture of a woman smiling and hanging an arm off of a piece of lab equipment. She is wearing an olive green 500 Women Scientists t-shirt over a black collared long-sleeved shirt.

Spring 2020 Updates

2020 has … gone in a very different direction than the way we probably all thought that it would back in early January. The emergence of the SARS-CoV-2 (COVID-19) pandemic has dramatically altered the way we live our day-to-day lives, and the way we think about ourselves as a global community. To reduce the transmission of the virus, the University of Maine, and many other schools and institutions, made significant alterations to their operating policies over spring 2020. This included sending students home (where possible), moving classes to online instruction only, asking faculty to work from home, and restricting laboratory and field work. This has resulted in some disruption to my plans, so here’s an attenuated post about updates over the last few months.

Teaching

The courses I am teaching this spring lent themselves well to being taught strictly online, with some modifications. Naturally, the presentations class works better in person where the stress of having an audience present promotes in situ training. The students were able to give an elevator speech, a regular short presentation for a peer-level audience, and a peer-level audience presentation with random technical challenges introduced by me into the slides. The remaining portion of the semester was devoted to giving presentations to a public-level audience, which requires a different presentation style and a good deal of thought into how much info is condensed and what you can and can’t expect your audience to already know. It was going to be too logistically challenging to organize public presentations remotely with short notice, so instead I had students create annotation notes for someone else’s slides, described here.

The data analysis class was easier to adapt, but required adjustment nonetheless. Instead of hosting a three-hour video meeting each week, I recorded the remainder of my lectures and made them available well in advance, so that students could watch and listen when they had time and internet access. During the class period, the class met to collaboratively work through data, which was always the goal, but with the challenge of remote work some re-imagination of the assignments was needed to allow students to opt-in to some of the work at times convenient to them.

To simplify the work, instead of having students independently perform similar analyses on different sets of data, I had them perform similar, somewhat independent, analyses on the same dataset, allowing them to all work collaboratively. As a bonus, this unpublished dataset was one that I have been working on collaboratively over the past year, so the students will be able to opt-in to participating in the publication of this work. This is in addition to the two manuscript which are slated to be submitted for review in the next few months, and two more under development. Because that’s still in development, I won’t share more detail now, but stay tuned to those results, and a more in-depth discussion on integrating student data analysis education with research.

Looking ahead, I am making plans to teach my fall classes online as well, including AVS 254: Introduction to Animal Microbiomes, and AVS 401 Senior Paper.

Research

Since starting at UMaine in September 2019, I have been working on establishing my lab. Most of that effort thus far has revolved around rearranging my lab spaces and acquiring specialized lab equipment. This aspect hasn’t been negatively impacted, outside of the new logistical challenges of delivering large pieces of equipment to locked buildings without coming into contact with delivery drivers.

However, acquiring supplies has been impacted, as certain materials are suddenly in extremely high demand, while production of others has dramatically reduced for the time being. Although I hadn’t begun any wet lab research which needed to be halted, I was just about to start culture work and training students on laboratory protocols, which has now been delayed for at least two months. Instead, I am in the process of transitioning student projects from benchtop-based to data analysis-based, at least for those students planning on graduating between now and spring 2021.

I am also focusing on trying to get previously completed projects written up and sent out for review, including a study on bacterial communities around window components in hospital rooms with the BioBE lab, a few collaborations on gut microbes in different animal species with the Yeoman Lab, and two more papers on the effect of climate, farming system, weed competition, and plant health on wheat production and wheat-associated soil bacteria with the Menalled/Seipel Lab. You can read the pre-print (meaning it hasn’t been peer-reviewed yet) on the soil microbes one here.

I do have some concrete exciting news, though, two graduate students will be joining my lab this summer/fall to start work on master’s of science degrees! Johanna Holman will be working on diet and gut microbiome in humans, for a master’s in Nutrition and Food Science, and Sarah Hosler will be working on new methods for investigating gut microbial communities in animals, for a master’s in Animal Science.

Looking forward, I’ll be changing my plan for training students on laboratory work, to facilitate social distancing measures while ensuring that students aren’t alone in the lab. Luckily for me, my labs and soon-to-be-office have windows between them so I can hover from a different room entirely.

Outreach

Social distancing has temporarily impacted my outreach activities, particularly in the short term as we try to adjust. A lecture I had planned for the Maine Organic Milk Producers annual meeting was canceled in April, although I’ll now be able to talk about Microbes and Social Equity at the Institute for Health in the Built Environment Industry Consortium annual meeting in May since it has been moved from in-person to online. Similarly, I am participating in a few discussions for other summer events and whether they might be transitioned to online formats. In the mean time, I’ve been practicing coming up with pithy interactions on Twitter.

A number of scientific conferences which I was planning to attend and/or have research presented at have made the decision to postpone, including the American Society for Microbiology’s Microbe 2020, International Society of Microbial Ecology’s ISME18, the Gordon Research Conference’s Microbiology of the Built Environment (MoBE) 2020 meeting, the American Society for Nutrition 2020 meeting. Other scientific conferences are attempting to switch to online formats, such as the Ecological Society of America (ESA) 2020 meeting, but bringing thousands of participants together in an interactive way is an extremely ambitious adaptation in such a short period of time.

Looking forward, I hope that many organizations will adjust and maintain their commitment to online accessibility of conferences, meetings, talks, and other outreach events, as well as making these resources available after the event. Attend a conference or public presentation is important to building you research program and improving the impact of your work, but financial, physical, logistical, or familial considerations often make it impossible to participate. Maintaining remote-accessibility, and making content available after the event, are important steps in making science more inclusive and allowing a broader audience to participate.