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!

Compost, food security, and social justice

What do compost, food security, and social justice have in common? They are all part of creating sustainable, more localized food systems that benefit the community. Want to know more? Check out the piece I co-wrote for The Conversation, along with two other soil microbe researchers.

City compost programs turn garbage into ‘black gold’ that boosts food security and social justice.” Kristen DeAngelis, Gwynne Mhuireach, Sue Ishaq, The Conversation. June 11, 2020

Dr. Kristen DeAngelis is an Associate Professor who studies microbes in soils, climate change, and human impacts, and Dr. Gwynne Mhuireach, a post-doctoral researcher who studies microbes in soils in the built environment and human health.

Woman with yellow background in a video meeting.

Microbes and Social Equity presentation at IHBE Build Health 2020 virtual meeting

I presented at my first virtual conference; the Institute for Health in the Built Environment Build Health 2020 industry consortium meeting on May 14, 2020.

Comprised of the Biology and the Built Environment Centerthe Energy Studies in Buildings Laboratory, and Baker Lighting Lab, IHBE connects researchers, practitioners, and designers engaged in creating healthier buildings. For the past few years they have hosted a mini-conference in Portland, Oregon in May, but this year a virtual format was a safer choice.

IHBE meeting organizers did a fantastic job at facilitating a remote meeting with a dozen speakers across multiple time zones. This included creating formatted slide decks for speakers to populate, coordinating sections by colors and symbols and providing respective virtual backgrounds for section speakers to use, and use of breakout rooms for smaller discussion groups.

I presented “Framing the discussion of microorganisms as a facet of social equity in human health“, and you can find a recorded version of the presentation here. There are no closed captions, but you can read the audio as annotations here:

The concept of “microbes and social equity” is one I’ve been playing with for a little over a year, and has developed into a colloquium course at the University of Oregon in 2019, an essay in PLoS Biology in 2019, and a consortium of researchers participating in “microbes and social equity part 2”. The Part 2 group has been developing some exciting research events planned for later in 2020, and those details will be forthcoming!

Podcast interview on the Maine Beacon

This week, I chatted with Mike Tipping, Communications Director of Maine People’s Alliance, and Ben Chin, Deputy Director of Maine People’s Alliance, on my recent publication on ‘microbes and social equity’ in PLoS Biology and the blog version found in the Conversation. We chat about social policies currently under discussion and how they can impact your microbes, why you should care about your neighbor’s microbes, and steps you can take to be a mire microbially-minded and socially-minded community member.

Check out the podcast here:

You can catch up on previous interviews at these fine outlets:

Microbes and Social Equity essay published!

I’m pleased to announced that the ‘microbes and social equity’ paper has been published as an essay in PLoS Biology, and will be included in their Microbiomes Across Biological Systems special issue.

In summer 2019, I developed and taught a course on ‘Microbes and Social Equity‘ to the Clark Honors College at the University of Oregon. The course assignments were literature review essays on various topics, which were compiled into a single manuscript as the group-based final project for the course. This large version is available as a preprint; however, the published version is more focused.


Framing the discussion of microorganisms as a facet of social equity in human health.

Suzanne L. Ishaq1,2*, Maurisa Rapp2,3, Risa Byerly2,3, Loretta S. McClellan2, Maya R. O’Boyle2, Anika Nykanen2, Patrick J. Fuller2,4, Calvin Aas2, Jude M. Stone2, Sean Killpatrick2,4, Manami M. Uptegrove2, Alex Vischer2, Hannah Wolf2, Fiona Smallman2, Houston Eymann2,5, Simon Narode2, Ellee Stapleton6, Camille C. Cioffi7, Hannah Tavalire8

  1. Biology and the Built Environment Center,  University of Oregon
  2. Robert D. Clark Honors College, University of Oregon
  3. Department of Human Physiology, University of Oregon
  4. Charles H. Lundquist College of Business, University of Oregon
  5. School of Journalism and Communication, University of Oregon
  6. Department of Landscape Architecture, University of Oregon
  7. Counseling Psychology and Human Services, College of Education, University of Oregon
  8. Institute of Ecology and Evolution, University of Oregon

Abstract

What do ‘microbes’ have to do with social equity? On the surface, very little. But these little organisms are integral to our health, the health of our natural environment, and even impact the ‘health’ of the environments we have built. Early life and the maturation of the immune system, our diet and lifestyle, and the quality of our surrounding environment can all impact our health. Similarly, the loss, gain, and retention of microorganisms ⁠— namely their flow from humans to the environment and back⁠ — can greatly impact our health and well-being. It is well-known that inequalities in access to perinatal care, healthy foods and fiber, a safe and clean home, and to the natural environment can create and arise from social inequality. Here, we focus on the argument that access to microorganisms as a facet of public health, and argue that health inequality may be compounded by inequitable microbial exposure.

‘Microbes and Social Equity’ essay accepted for publication!

Over the summer, I taught a class on “Microbes and Social Equity” at the University of Oregon, the culmination of which was a joint paper I wrote with the class and several of the guest speakers. After soliciting several journals and modifying the scope a bit, I’ve just heard back that it has passed peer-review and been accepted for publication as an essay in PLoS Biology!

I’ll be sure to send out the link and more information when it’s online.

Microbes and social equity preprint available!

Framing the discussion of microorganisms as a facet of social equity.

Suzanne L. Ishaq1,2*, Maurisa Rapp2,3, Risa Byerly2,3, Loretta S. McClellan2, Maya R. O’Boyle2, Anika Nykanen2, Patrick J. Fuller2,4, Calvin Aas2, Jude M. Stone2, Sean Killpatrick2,4, Manami M. Uptegrove2, Alex Vischer2, Hannah Wolf2, Fiona Smallman2, Houston Eymann2,5, Simon Narode2, Ellee Stapleton6, Camille C. Cioffi7, Hannah Tavalire8

  1. Biology and the Built Environment Center,  University of Oregon
  2. Robert D. Clark Honors College, University of Oregon
  3. Department of Human Physiology, University of Oregon
  4. Charles H. Lundquist College of Business, University of Oregon
  5. School of Journalism and Communication, University of Oregon
  6. Department of Landscape Architecture, University of Oregon
  7. Counseling Psychology and Human Services, College of Education, University of Oregon
  8. Institute of Ecology and Evolution, University of Oregon

Abstract

What do ‘microbes’ have to do with social equity? On the surface, very little. But these little organisms are integral to our health, the health of our natural environment, and even impact the ‘health’ of the environments we have built. Early life and the maturation of the immune system, our diet and lifestyle, and the quality of our surrounding environment can all impact our health. Similarly, the loss, gain, and retention of microorganisms ⁠— namely their flow from humans to the environment and back⁠ — can greatly impact our health and well-being. It is well-known that inequalities in access to perinatal care, healthy foods and fiber, a safe and clean home, and to the natural environment can create and arise from social inequality. Here, we frame access to microorganisms as a facet of public health, and argue that health inequality may be compounded by inequitable microbial exposure.


In just a four-week course, I introduced 15 undergraduates from the University of Oregon Clark Honors College to microorganisms and the myriad ways in which we need them. More than that, we talked about how access to things, like nutritious foods (and especially fiber), pre- and postnatal health care, or greenspace and city parks, could influence the microbial exposures you would have over your lifetime. Inequalities in that access – such as only putting parks in wealthier neighborhoods – creates social inequity in resource distribution, but it also creates inequity in microbial exposure and the effect on your health.

By the end of the that four weeks, the students, several guest researchers, and myself condensed these discussions into a single paper (a mighty undertaking, indeed).

And now that I’ve found a preprint server that accepts reviews/commentaries, it’s available for preview! The paper is currently under review and will be open-access when eventually published.

During the course, a number of guest lecturers were kind enough to lend us their expertise and their perspective: