Category: Perspective

Blending art, science, and cheese in Venice at an Interdisciplinary workshop

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We’ve all felt the thrill of synchronicity when meeting someone for the first time and realizing how we have much in common, but when this occurs for a dozen people simultaneously, who go on to share ideas and excitement for 13 hours straight, it’s magic. Thus, Professor of Anthropology, Roberta Raffeta’, created magic when she invited a group of microbiome and health science researchers together for the “Integrating Qualitative and Quantitative Data in Microbiome Research and Postgenomics: Toward an Interdisciplinary Dialogue” workshop at the Università Ca’ Foscari Venezia. Roberta works with many disciplines, including microbiome, computational, health, and social sciences, and her work often focuses on how research is designed, implemented, and interpreted. Her work across disciplines gives a larger view on how different disciplines approach similar research, as well as provides her with a rich network of colleagues.

The workshop was in the spirit of a project that Roberta, Prof. Nicola Segata, Prof. Elena Bougleux, and others investigating the sharing of microbes at Antarctic stations based on social interactions and shared spaces. That project is a clear example of how social systems can determine who you interact with, where, and how, and thus which microbes might get shared between you or between everyone at the base. While those data were still being processed and not shared, we did get to hear a bit about the journey to Antarctica from Elena.

After introducing the project, workshop, and ourselves, we began with a presentation by Professor Federico Russo. Her talk focused on how health is quantified, and how that alters the way we design and perform health research. Health is a complex concept that has biological, chemical, physical, and social aspects which can be measured and metric-ified. For example, there are bio-logical versus bio-social metrics of health (social effects of disease, feelings about health and outlook), and everything in between which can be measured to assess the state of health or disease. In addition, health research uses the term “social determinants”, which is similar to what biologists, microbiologists, or ecologists mean when using the term “environmental factors”, but these often refer to the same thing. These factors are the collection of host, social/community, environmental, and geological features which affect who you are and what you encounter in your life. Some of them seem very specific, like age, but the expression of age can be modified by staying active, eating well, managing stress, and avoiding pollution, so on its own, knowing someone’s age might not be useful information.  Thus, to study health, we use both markers, like age, to tell us potential outcomes or indicators of one’s health state, and social determinants, like lifestyle features, to tell us possible causes or mitigating factors of health.

Yet, one cannot slice the concept of health into a thousand measurable factors and then expect to re-assemble them back into the concept it was – because what makes us feel well or healthy is not necessarily having or knowing that our biological metrics are good, it’s feeling well even if our biological markers are out “normal” parameters or when, on paper, we are sick.  This brings up a concept that I had discussions about within this workshop group, with the faculty at Ghent, and with researchers through MSE and MiSt: that your social factors and the support network around you strongly influence whether you feel well or unwell, regardless of what your biological markers would suggest.

There is also a focus in healthcare on regaining health when someone is sick, with social or institutional support system for that (rehabilitation clinics, etc.), but there is not always an institutional focus on understanding how people stay healthy, in part because this is seen as a personal choice and not a result of adequate access to public resources (fresh food, water, air, shelter, education, safety), or as a function of useful public health policies which make is easy for people to take care of themselves. Simple features like sidewalks, bike paths, local grocery stores, free public restrooms, shade and places to sit, are all features that allow people to stay active, get around, stay healthy, and use their public spaces.

My research talk was next, and I focused on the steamed broccoli sprout intervention trial I completed a few years ago with Yanyan Li. That was a pilot study, which recruited 20 people to steam and eat broccoli sprouts every day for a month, to measure any changes in the gut microbiome, the metabolites it was producing, and whether gut bacteria would convert the inactive glucoraphanin in sprouts into the anti-inflammatory compound sulforaphane. Rather than focus on the microbiological, metabolomic, or diet survey results, I presented everything which went unexpectedly in the study, and what people told us about the challenges to consuming daily sprouts. This, in fact, was the real goal of the study, to understand which aspects of the diet would be challenging, or rewarding, and to try and make things as easy as possible. My observations on the diet study sparked excellent discussion, which gave me plenty of ideas on framing the scientific manuscript and what we learned from our participant’s data, as well as a perspective piece on the design and implementation of the study and what we learned from our participants’ feedback (not their data).

Another study observation which was also a reoccurring workshop discussion was the need for health studies that start with people’s perspectives and patient’s identification of problems, which then work backwards to understand how the microbiome is involved. This style of research is case-study and health engineering research to test applied research questions, and is needed in addition to the large-scale, double-blind experiments to test basic research questions. We talked at length about how most large-scale diet surveys are inadequate, no matter how detailed they are, because they become so vague as to be useless when they are generalized to ask about all possible food item diets. Most diet surveys that are meant to be broad ask for too much detail about things which are considered superfluous for individual research projects, and too little detail on critical info. For example, most diet surveys that gather diet history (eating habits over the last 6 – 12 months) are underpowered to assess fermentation products, don’t ask how  people cook and make decisions about diet, and are quantified to assess compliance to an idealized and single idea of a healthy diet, even if it doesn’t work for every person (ex. dairy is good on many diet surveys but there is no place to select that you don’t consume dairy because you are allergic to it).

This discussion carried across lunch, during which we diverged into many animated conversations only to bring it back to quality of information in the presentation after lunch, by Professor Lisa Lehner, a health researcher who presented reflections on three research projects, in which the availability and completeness of data about patients was lacking, and this stymied researchers’ attempts to understand public health for three disease models, such as how these diseases are transmitted, how people access health care, and how migration, homelessness, or simply traveling often can impact access to care. For example, in trying to study human papilloma virus cases, her research found that country of sampling was included in patient records but not country of infection. Similarly,  the idea of “where do you live”, “where are you from”, or “where have you been recently where you might have contracted this infection” are very different questions with different contexts to the answers, not all of which will provide useful information for this specific study depending on which the patient was asked and what their history was.

Information sharing is both the key and the challenge, and we discussed how often the information to resolve public health crises exists, but it’s not all in one place, it’s missing information, it doesn’t contain the right context, institutions don’t want to share, some information is private or access is limited even to medical providers, some information is not retained, and even when we get much of this in one place the amount of detail is overwhelming to the point where researchers need to spend years trying to figure out how to make it useful – what’s important to know? What is a ‘red herring’? — before it even gets to be used for infection tracking, treatment, and prevention. Her research also highlighted inequities in healthcare, and that sometimes information that would help us understand infection data can’t be made public, because you might reveal information about sensitive populations that can be used for discrimination. For example, people without health insurance might be migrants that are no longer on active visas, and quantifying how many people can make them a political target.

The discussion after the talk was so engaging, and blended into the focus of another speaker, so we informally heard from Professor Donato Giovannelli, who was not able to present his talk (yet!) because the workshop was running later than expected (we all had so much to talk about!) and he had to catch a train. Donato is a geomicrobiologist examining microbes in extreme environments to understand how they survive and function. He has a particular focus on the microbial fixing of gaseous hydrogen which produces water, and how biological sinks for freshwater (like us walking, talking, water bottles), actually allow for the preservation of large quantities of water on Earth. Donato’s short version of his talk was focused on the scale of standardization in research. He argued that what works in the lab or the field changes based on the needs and circumstances of each project, so you need to thoroughly describe what you did but that doesn’t mean every lab uses, or has to use, the exact same protocols, kits, or methods every time. In fact, even if it were possible to replicate circumstances exactly, trying to do everything identically will just make all studies biased in the same ways. There is no way to replicate some experiments, especially with humans, because no human is ever replicable, even to ourselves.

Highlighting the importance of methods and process in research brought up another challenge in research: it is important to include vocabulary to describe what you mean, in addition to what you did, but Methods sections are often compressed by scientific journal word limits, and all the nuance and context or the problem-solving portion, gets cut for space and is over compressed to the point of being useless. Donato argued, as many scientists do, that the explanation of the methods should be the majority of the paper, and many labs do publish the long form of the methods as a co-published paper, or as a protocol paper that gets cited in the whole scientific experiment paper. Our workshop heartily agreed. Science is a process, as scientists we are creating this process and this is our most valuable contribution, more so, even, than the results.

Sometimes the drive for standardization also leaves out people who contributed to the study in a way, but their contribution is considered “not science”. For example, technicians, field personnel, or anyone who helped you access or collect samples but did not work on the samples or contribute “conceptual framing or interpretation” don’t count as authors under most journal guidelines, even if you could not have done the project without them. Similarly, if you designed your project based on feedback and direction from the public or specific audiences, this is somehow not considered “conceptualization” or experimental design (???!!!). It is always up to the author team to decide who is and isn’t an author, but without more flexible guidelines on authorship, it can be easy to remove someone’s contribution to a publication.

This type of value judgement in science segued us to our last presentation of the day, on how the terms/definitions we use, the factors we choose to study, the things we prioritize in our research, all reflect values we have placed on some things over other. It can also, unintentionally and intentionally, place inherent value on having certain study results or outcomes. And when the study is about people, placing value judgements on biological, microbiological, or social factors can create a hierarchy – you can see where I am going with this – in which certain people are implied to have superior metrics. This is something a research team and I published on in microbiome research, and has been the focus of a multi-year project led by Professor Abigail Nieves Delgado, Dr. Aline Potiron, and others, on how microbiome scientists define terms which are used to describe people, and how those definitions carry assumptions that may influence the interpretation of the results by researchers or readers.

Population descriptors are ways of, well, describing populations. However, the selection of terms, how you define them, how you categorize those terms, are often too strict to be applied to real-life people or in different communities. Using the same example of age, how do you compare age in two populations with wildly different exercise, diet, or stress load which all impact the physical or behavioral expression of age? More to the point of this talk, how do you categorize ancestry without nuance? Do you focus on genomics, or culture, or both? Do you place people in categories based on certain factors, or let them choose their own? How do you compare people in one location to another without considering the history of war, colonization, and slavery had on the ability of people to choose with whom to have children? And does ancestry even matter when you consider the myriad changes to health and the microbiome effected by what you eat, what animals and people you interact with, and where you live? Scientists all working on the human microbiome had wildly different understanding or definitions of population descriptors, and beliefs around what population descriptors were caused by or caused changes to the microbiome. And this, despite most microbiome studies having little to no need for information on ancestry or race to answer their research question.

Studies don’t gather data on every possible factor in people, that would require a detailed biography of every participant. Researchers choose what type of data to collect about someone based on what is important to the study and answering the research question – but as researchers we tend to think within the constraints of our own discipline – what info do I need for my statistics or to publish in my field? When that happens, we compress the variability of the people we study into fewer dimensions, example like taking an in-person experience at the beach and representing it as the words “seashells”, “gritty floor”, and “wet”.

Finally, a theme that came up several times during the workshop was that human social structure or institutions sometimes have so many constraints as to fail in their mission to provide resources to the public. As a perfect example, we did not have air conditioning at the university, even though was 85 degrees outside and between 90 and 105 degrees F inside some of the rooms after we had been in them for a while, because it is university policy to turn air conditioning on for the whole campus only after a certain date regardless of what is going on in real life. I don’t want to pick on the university, because this is a very common policy at universities, including UMaine. But it highlights the point that solutions (to air conditioning, microbiomes, health, etc.) need to be nimble enough to respond to local conditions using the input of people who are actually living through those conditions. And in this way, we have the crux of the workshop: how do we perform local-conscious and nimble science that is driven by the needs of actual living things or ecosystems, against the tide of institutional habit? For me, that’s going to involve more community-based and person-driven research questions, more collaboration with this remarkable group of researchers, and hopefully a lot more fresh, Italian mozzarella.

Ideation in Ontario

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Last week in Guelph, Ontario, Canada, I had the unique please of “nerding out” with long-time colleagues (who I was meeting in-person for the first time) about microbial ecology questions that we wanted to answer, the science fiction we were reading, which metal band to listen to for the winter holidays, how to perform large-scale research on a tight budget, and whether the next season of whatever show had piqued our interest would be any good. The nerds-in-question are the Microbiome Stewardship research group, led by the intrepid Kieran O’Doherty, that I’ve been a part of for the past few years (and longer, counting the time we’ve collaborated through the Microbes and Social Equity working group).

Group photo of Left to right; front: Zhongzhi (Michael) Sun, Emma Allen-Vercoe, Sue Ishaq; middle: Mikaela Beijbom, Mallory Choudoir, Sarah Elton, Kieran O'Doherty, Panuya Athithan; back: Grace Gabber, Andreas Heyland, Rob Beiko.
Left to right; front: Zhongzhi (Michael) Sun, Emma Allen-Vercoe, Sue Ishaq; middle: Mikaela Beijbom, Mallory Choudoir, Sarah Elton, Kieran O’Doherty, Panuya Athithan; back: Grace Gabber, Andreas Heyland, Rob Beiko.

Over two days, my microbiome stewardship colleagues and I (both original team and expansion pack researchers) shaped our concept of what it means to share microbes between individuals, communities, and ecosystems; what it would mean to consider microbes as a natural resources to which everyone had an innate right to; and how it would look for public and planetary health to reduce the harm of human industry and consumerism to live more sustainably and regain all the benefits that the microbial world can provide us. Our of this meeting, we imagined what the focus of our next year or two of research will look like, as individual researchers and as a group, as we embark on the next phase of our multi-year project: case studies of how microbiome stewardship could be tailored, implemented, and evaluated. These studies will be published as they are completed and pass peer review, in a scientific journal online (announcement forthcoming).

This research ideation meeting followed two years of conversation, presentations, a symposium (sessions can be viewed here), journal articles, and a whole lot of research-, personnel-, and travel-coordination on the part of our research wrangler, Mikaela Beijbom, who has been helping us to organize our words and activities for the past 8 months.

As this tumultuous and combative year comes to a close, and as I prepare to end the “break” which was my semester-long sabbatical and return to 50-hour work weeks, the precious opportunity to let our minds wander – through work, life, and play – was a brief return to the pure joy of scientific discovery which drew us all to our careers. This year, scientists have faced hurdle after hurdle placed by the very public research institutions which were created to help us seek knowledge on behalf of the public good. Funding cuts have reduced the scientific workforce; lost precious time, expertise, and data; and disrupted the innovation and ideation process which research forges. Yet, the time I spent with colleagues last week was a reminder that knowledge generation, public good, scientific inquiry, and collaboration are values which cannot be defunded, banned, or curtailed so easily. As for our group, we’ll keep meeting (virtually, at least) throughout 2026 and beyond, for the love of science.

Article published on the use (and mis-use) of human population descriptors as biological determinants of human microbiomes!

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Since the summer of 2023, I have been part of an interdisciplinary team that examines the way microbiome researchers use social and population descriptors for people in their analysis. In many cases, only basic information about a person is available in large datasets that are publicly available to use, or detailed information about a person is difficult to obtain during a study, thus many researchers rely on “proxy terms” to try and understand how human microbiomes are assembled and changed. Proxy terms are broad categories that group people, such as geographic area or race, but often these are too broad to be used for any meaningful analysis, especially when working with biological data.

‘Race’ is a relatively new concept used to describe social groups, and as discussed brilliantly in the National Academies of Science, Engineering, and Medicine’s report on “Use of Race, Ethnicity, and Ancestry as Population Descriptors in Genomics Research“, it has been mis-used for several hundred years to insinuate basic biological differences between people. This was done intentionally to justify discrimination all the way up to slavery, but it has been unintentionally propagated into research through the use of race as a proxy term to represent someone’s lifestyle. In recent decades, microbiome research has been trying to understand how human lives affect the microbiomes they accumulate, and similarly has sometimes incorrectly espoused the idea that vague social categories manifest as biological differences.

Our group delved in the history of race in biological science, case studies where results that implicate race led to discriminatory policy and practice, and give guidelines for selecting more specific factors to understand the social and environmental impacts on the microbiome.

I’m pleased to announce that we just had our review published in mSystems: ” Prioritizing Precision: Guidelines for the Better Use of Population Descriptors in Human Microbiome Research.” We presented this work at the 2024 Microbes and Social Equity speaker series, too, and the recording can be found here. It builds off of our collective work over the past decade.

Nicole M. Farmer, M.D.,

Amber Benezra, PhD.,

Katherine Maki, PhD.,

Sue Ishaq, photo courtesy of Patrick Wine, 2021.

Sue Ishaq, PhD.,

Ariangela Kozik

Ariangela Kozik, PhD.,

“ Prioritizing Precision: Guidelines for the Better Use of Population Descriptors in Human Microbiome Research.“

Authors:  Nicole M. Farmer1,2, Amber Benezra1,3, Katherine A. Maki1, Suzanne L. Ishaq1,2, Ariangela J. Kozik1,2,4,5* 

Affiliations:

1 The Microbes and Social Equity working group, Orono, Maine, USA; 2 Nova Institute for Health, Baltimore, MD; 3 Science and Technology Studies, Stevens Institute of Technology, Hoboken, New Jersey, USA; 4 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA; 5 Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA

Abstract

Microbiome science is a celebration of the connections between humans, our environment, and microbial organisms. We are continually learning more about our microbial fingerprint, how each microbiome may respond to identical stimuli differently, and how the quality of the environmental conditions around us influences the microorganisms we encounter and acquire. However, in this process of self-discovery, we have utilized socially constructed ideas about ourselves as biological factors, potentially obscuring the true nature of our relationships to each other, microbes, and the planet. The concept of race, which has continuously changing definitions over hundreds of years, is frequently operationalized as a proxy for biological variation and suggested to have a real impact on the microbiome. Scientists across disciplines and through decades of research have misused race as a biological determinant, resulting in falsely scientific justifications for social and political discrimination. However, concepts of race and ethnicity are highly nuanced, inconsistent, and culturally specific. Without training, microbiome researchers risk continuing to misconstrue these concepts as fixed biological factors that have direct impacts on our microbiomes and/or health. In 2023, the National Academies of Sciences, Engineering, and Medicine released recommendations on the use of population descriptors such as race and ethnicity in genetic science. In this paper, we posit similar recommendations that can and must be translated into microbiome science to avoid re-biologizing race and that push us toward the goal of understanding the microbiome as an engine of adaptation to help us thrive in a dynamic world.

White paper and perspective published on “Running a queer- and trans-inclusive faculty hiring process”!!

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I’m delighted to announce the public release of a white paper on queer- and trans-inclusive faculty hiring practices, and a perspective piece introducing it!! This is the culmination of months of writing by an international group of talented scientists led by Dr. JL Weissman, and I was honored to participate in these and future efforts from the group.

The newly-formed group, Advancing Queer and Trans Equity in Science (AQTES), wants to improve the field of research by making the hiring process fair and welcoming for everyone. No matter what your personal identity is, we can all agree that fair and unbiased job searches are critical to hiring the best talent. But, sometimes a poorly-organized job search prevents the people with the best talent from applying at all.

In our white paper, we give suggestions on how to host a job search that is better for everyone. We provide examples and advice on how to write job adverts, create the agenda and atmosphere for the job search, how to make the interview process more accessible for everyone by remembering that we are humans and not robots, and how to support your new faculty.

Running a queer- and trans-inclusive faculty hiring process.

Authors

Weissman, JL, Chappell, C.R., Rodrigues de Oliveira, B.F., Evans, N., Fagre, A.C., Forsythe, D.,  Frese, S.A., Gregor, R., Ishaq, S.L., Johnston, J., Bittu, K.R., Matsuda, S.B., McCarren, S., Ortiz Alvarez de la Campa, M., Roepkw, T.A., Sinnott-Armstrong, N., Stobie, C.S., Talluto, L., Vargas-Muñiz, J., Advancing Queer and Trans Equity in Science (AQTES).

Abstract

Queer and transgender scientists face documented systemic challenges across the sciences, and therefore have a higher attrition rate than their peers. Recent calls for change within science have emphasized the importance of addressing barriers to the success and retention of queer and trans scientists to create a more inclusive, equitable, and just scientific establishment. Crucially, we note these calls come primarily from early career researchers; relatively few queer and trans scientists have passed through the gauntlet of the faculty job search to become faculty ourselves, which is typically key to long-term persistence in academia. Our lack of representation creates a self-reinforcing cycle in which queer and trans trainees do not see our needs considered in established processes and power structures. Moreover, this status quo has historically been and continues to be harmful, disproportionately impacting those of us who have multiple intersecting marginalized identities. Here, we provide concrete guidance to search committees to support queer and trans candidates throughout the faculty selection process based on our personal experiences as early career scientists who have been on the job market.

Graphics in the post and the article created by Callie R. Chappell.

Citations

Citation for the paper: Weissman, JL, Chappell, C.R., Rodrigues de Oliveira, B.F., Evans, N., Fagre, A.C., Forsythe, D.,  Frese, S.A., Gregor, R., Ishaq, S.L., Johnston, J., Bittu, K.R., Matsuda, S.B., McCarren, S., Ortiz Alvarez de la Campa, M., Roepkw, T.A., Sinnott-Armstrong, N., Stobie, C.S., Talluto, L., Vargas-Muñiz, J., Advancing Queer and Trans Equity in Science (AQTES). 2024. Running a queer- and trans-inclusive faculty hiring process. EcoEvoRvix repository 6791.

Perspective piece introducing the paper:  Weissman JL, Chappell CR, Francesco Rodrigues de Oliveira B, Evans N, Fagre AC, Forsythe D, et al. (2024) Queer- and trans-inclusive faculty hiring—A call for change. PLoS Biol 22(11): e3002919.

This work is being presented at the American Geophysical Union annual meeting in Washington DC in December, in the session on “ED12A: Advances and Progress Toward a More Inclusive, Diverse, Equitable, and Accessible Scientific Community II”.

This work is being presented as a seminar at the Microbes and Social Equity working group virtual seminar series, Dec 20th, 2024. Registration is free but required.

Featured on the GW Integrative Medicine podcast!!

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I was interviewed by Leigh Frame and Janette Rodrigues for the GW Integrative Medicine podcast! Leigh Frame is an associate professor and Janette Rodrigues is the OIMH Admininstrative Director at the George Washington (GW) University School of Medicine and Health Sciences, and they host the podcast to explore research on health.

We talked about my work on broccoli sprouts and gut microbes, Microbes and Social Equity, and Microbiome Stewardship. You can listen to the episode here.

Featured on the Microbial Matters podcast!!

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I was interviewed by Dr. Mark Martin for the Microbial Matters podcast! Mark is a renowned microbiologist who has long has a presence online making science accessbile to everyone. The show features exciting and fun conversations with researchers about their work on tiny organisms with a global impact.

I’ve linked to the Youtube video version below, but you can download the video/audio for my episode, link to podcast services, and find the show notes by clicking here.

The value of choosing when, and how, and how much to think about work

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It has been a long time since I have written a reflection-style blog post (as opposed to simply sharing updates and events), and for good reason — I have been overcommitted for my time during (at least) the past year and half and have had little left over for the imagination-based portions of my work. I love what I do and I routinely choose to spend my free time on it, but with the increase in demands for my attention I have lost the freedom to choose when, and how, and how much I think about work.

Many of the non-essential aspects of my job, such as creative writing on the blog, had to be paused to accommodate an increasing number of requests for my time on task-based items (emails, forms, admin, logistics, planning). While many of those requests were simple, the urgent or time-sensitive nature of resolving student, colleague, or university requests with impending deadlines required me to cycle rapidly through tasks/conversations each day, which is mentally taxing over extended time.

More than that, many academics and researchers have had to learn to multi-task even to the point of answering emails during meetings or engaging in multiple conversations simultaneously just to find time to respond to all of the requests for our help and expertise. It might be feasible in short bursts, but after keeping up this pace for so long I started to face burnout over the fall.

I’ve previously written about the value of having time to think in research careers. It is well-recognized that more time off and better-quality time-off (in which you are not just taking work with you to the beach) is needed. But, it is critical to recognize that resolving academic burnout requires universities to increase hiring for faculty and staff rather than cutting positions to lower budgets and redistributing the workload among remaining faculty and staff.

The “too-busy-to-think” problem in academia can never be resolved if we have so many components to our daily task list that we don’t have time to complete the very things we were hired to do: research and teach. To excel in these, we need time to think. Over the past week, I took several vacation days (filled with amazing adventures with friends not al of which is pictured here) prior to attending a small (< 150 people) conference for two days, during which I intentionally minimized the amount of multi-tasking I did while listening to presentations. I never truly stop thinking about my work; it is a part of my identity and I love the problem-solving activities I do, but having this precious time to choose what I consider or spend my time on, and being able to focus on what was in front of me, was immensely rewarding to how I create my own research as well as restorative.

A music band onstage, with a blurry crowd in the foreground.

One of those adventures that I remembered to take photos of was a concert. I was lucky enough to catch “Tank and the Bangas” perform live at Belly Up in San Diego. The band’s most recent album has been nominated for a Grammy Award, and their live performance was electric, passionate, and inspiring.

I was even luckier to spend time with the incredible Candace Williams, a friend and researcher at the San Diego Zoo. Candace took another friend of mine and I around the park (most of which is not pictured here), and I really enjoyed the opportunity to hear about and see her work on rhino gut microbiomes in this setting.

Sue and Candace Williams standing in front of green foliage.
A view of the open enclosure for herbivores in the San Diego Zoo Safari Park.

One of the main reasons for my trip was to attend the 3rd CMI International Microbiome Meeting (CIMM) at the Center for Microbiome Innovation at UC San Diego. The conference was held at the Scripps Institute for Oceanography in La Jolla (just north of San Diego), and the long pier shown in the distance in the photo below is one of their state-of-the-art research facilities. I’ve wanted to visit the Institute for the past few years but have not had the opportunity to travel there.

Some other conference attendees and I got a tour of the pier from Jack Gilbert, who is the Deputy Director for Research and Associate Vice Chancellor for Marine Sciences there. Jack is also the Editor in Chief for the scientific journal mSystems, and has been a major supporter of my career and the Microbes and Social Equity working group for the past two years. It was awesome to finally meet Jack in person!

Having a small conference venue, and multiple meals and networking events on-site during the day, meant that I had plenty of time to chat with Jack and other storied researchers in my field. For example, I chatted about my work on scallop microbes as well as my unique conference-fashion combinations with one of the foundational researchers in host microbiology. I got ample opportunity to meet with peers and science celebrities-in-the-making, and even to re-meet Dimitry Krementsov, whom I had originally met way back in 2008 due to overlapping friend groups in Burlington, Vermont, well before I went to grad school or though about microbes. It turns out that not only do we have complementary research interests that we’ll be following up on, but had unknowingly shared mice recently through a collaborator we have in common.

The talks on the first two days of the event (I did not attend the third day as it was outside the scope of my work) ranged from gut microbiome, to diet, to agriculture, to the ocean, and because the presentations times were long the researchers were able to tell better stories about their science and progress through their thought process over time. As an early-career researcher, I enjoyed their perspective on the process of discovery. I enjoyed all the presentations, but a few in particular resonated with me. For example, a talk on gut immunology reflected on the idea that commensal bacteria have been anthropomorphized as friendly to us when in reality the commensalism arises from our immune system setting good boundaries for those relationships, which has me thinking about my own work on disrupted gut microbial communities. Rosie’s work on microbes in aquaculture-managed oceanwater got me thinking about how curating agricultural/aquacultural management practices within the context of working with an ecosystem can help reduce the negative impacts of those human activities while boosting production. And one talk on using plant biology and plant-microbe interactions to instill disease resistance in citrus plants was just awesome to hear about; I don’t work on plant microbiomes anymore but the research ideas were so novel to me that it sparked my curiosity and creative thought process.

I spent quite a bit of the conference with Candace with Rosie Alegado, during which we reflected on the scientific research being presented, the tastiness of the food served, and the immense value of ‘capacity sharing’ by inviting community members to participate in the design and performance of research.

Sue, Candace Williams, and

Rosie and Candace are both famous for their community-rooted research in ocean and wild animal microbiology, respectively, and I continue to learn and be inspired by them. Equally inspirational is Carla Bonilla (not pictured) who I caught up with (too) briefly while I was in San Diego. In addition to her research, Carla’s work on pedagogy and expanding our views of microbiology is one of the pillars of MSE.

I was also fortunate to spent quite a bit of time with Sean Gibbons and Jotham Suez, both prominent researchers on diet and gut microbiome who both presented their work. In addition to hanging out at the conference, we found time to go on several adventures. We caught the cherry blossoms in peak glory at the Japanese Garden in Balboa Park, as well as spend the day strolling around the rest of the park and La Jolla beach discussing research, judging coffee, laughing hysterically, perusing the art colony in the park, and meeting every dog within petting range. I can’t wait till the next round of shenanigans!

  • Sean Gibbons, Sue, and Jotham Suez posing on rock path in front of bright pink blooming cherry trees at a Japanese Garden.
    Jotham Suez, Sue, and Sean Gibbons at the Cherry Blossom Festival at the San Diego Japanese Garden.
  • A view down the underside of a concrete pier, with breaking waves and cloudy sky in the background and wet sand in the foreground.
    The underside of the research pier at Scripps Institute of Oceanography
  • Sue jumping in the air below a concrete pier, with wet sand in the foreground and breaking waves under cloudy skies.
    An action-shot below the pier where everyone takes a selfie.
  • A closeup of the sandstone cliff at La Jolla beach with green algae growing over the bottom several feet of the cliffs.
    The cliff near the Scripps Institute in La Jolla.

While I was in San Diego, I also went to a drag show with friends and colleagues. For anyone who is not familiar with ‘drag’, it can be presented in many ways but it always an artistic performance in which the performers adorn clothing, hairstyles, and makeup to create a persona for the stage. In the same way that actors don clothing, makeup, and more to create personas in order to tell a story, with drag the chosen persona plays on the idea of gender norms of what society thinks a person should wear or say based on which genitals they have. The performers often sing/lip sync, dance (including some extremely athletic moves while wearing high heels), perform stand-up comedy, read book aloud, or in the case of the show I just went to – host a game of bingo. However it is performed, drag engages in humor, pageantry, and the idea that how we look can be a form of artistic expression rather than the composite of other people’s opinions on how we should look or act. I can’t think of anything more wholesome than an event which welcomes everyone to be their authentic self. If you have never been to a drag show, I highly recommend it, and everyone is welcome at drag shows!

I have included some photos of a previous show I attended there, as I wasn’t able to get good photos of the performance this time (I do have an amazing group photo, but I wasn’t sure if my friends would want to be featured on my professional social media).

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The value of choosing when, and how, and how much to think about work
Several drag queens in elaborate gowns, hairstyles, and makeup, standing on a stage.

Overall, the combination of time to relax, to think, to share, and to have fun was an restorative and enjoyable way to make new friends, deepen connections with previous friends and colleagues, and to enrich my own research by learning from rockstars in my field. You’ll definitely find me at CIMM again next year!

*The title of this blog post is directly inspired by phrasing in Arundhati Roy’s novel, The God of Small Things.

iScience Backstory on our collaborative work on ants, nematodes, and bacterial transfer

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Over the summer, an article was published which featured a handful of researchers from across the US and research spanning a decade on the bacterial communities associated with invasive ants and nematodes in Maine. At the time, we were invited to also contribute a “Backstory” article to the scientific journal iScience which described the journey and the ideas.

That story authored by myself and Ellie Groden (senior researcher on the journal article) has just been published, and can be found here. I’d like to thank Dr. Sheba Agarwal, who was the editor on the paper, helped us develop our Backstory, and also spoke to me about this and other work as a guest on the WeTalkScience podcast.

How does an academic department decide on their courses?

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Now that I am an assistant professor, I perform scientific research, teach formal classes to undergraduate and graduate students, and I advise undergraduate students, as well as a smattering of other administrative or organizing-based activities. While I have performed nearly all of these in past job positions, the advising is a completely new aspect which has provided valuable insight into my other activities. The University of Maine serves a large number of undergraduate students, and many degree programs are specifically designed as preparation for specific career fields. Undergraduate students in my department now ask for my advice on which courses to take to best finish their degree, and this has led to some interesting discussions on why certain classes are required or not, and why certain classes are offered or not. I realized that the mechanics of course development are not well known to students, or even to academics who haven’t participated in it, and I thought I would share what I’ve learned.

Deciding on content

At the university level, courses are created and designed to offer a certain level of core material made up of basic concepts to introduce students to different fields of information; courses like introduction to biology, or general writing techniques. These may be referred to as ‘general education‘ courses and are designed for student audiences from many different programs at once. GenEd courses are taken in the first or second year of study in order to fill in any gaps from the very different high school educations students have, as well as teach the basics of information-finding and collaboration skills that they will need in other classes. GenEds are usually required before students take high-level courses in specific areas of study. Often, GenEds or introductory courses cater to hundreds of students per year, and there are several instructors to cover all the course sections, as well as teaching assistants, who provide instruction. There are additional core University requirements that each department can decide how to handle, such as the UMaine Capstone Experience requirement for students, which requires students to create a senior project related to their major. Within each academic department or unit (for example, Animal and Veterinary Sciences), there are core course requirements specific to that field of student that all students enrolled in that program need to take (for example, these requirements for Bachelor’s of Animal Science with a pre-veterinary concentration).

One factor in the decision about course content is simply which skills or knowledge students will need in order to enter the workforce related to their field of study. For example, undergraduate students who are intending to go on to a veterinary degree are often enrolled in pre-vet programs designed to prepare students for that further degree and to meet those application qualifications. As such, they will need to learn everything from anatomy to physics. Any content which is required to make the degree meaningful will also be required for students to pass in order to graduate, and means that it must be taught often enough that students have an opportunity to take it. Thus, core or required classes might be held at least annually, and sometimes multiple times a year. If the usual instructor is unable to teach it for a period of time, or there is turnover in the department, a temporary or adjunct instructor can be brought in on a short-term contract to ensure that course can be offered regularly.

Another factor is the area of expertise of the faculty instructors, who are research and/or teaching faculty with long-term contracts, such that those classes will be offered for at least as long as that person is employed. Because areas of expertise change over time, and because faculty come and go, this often drives the evolution of an academic department’s curriculum focus over decades. For example, I have a 50% research and 50% teaching appointment over a 9-month contract, which equates to 12 credits worth of teaching or formal mentoring in my department over the academic year. While I do teach some courses which were already set by the department, I had enough room in that 50% appointment to propose and teach two classes of my own design, one of which has now become a required course for animal science undergraduates specifically because my area of expertise has grown in importance and popularity in the past few decades. Departments will hire new faculty or instructors specifically because of their area of expertise and which direction they want the overall academic program to go in.

A more minor consideration on course content relates to university budget models, and whether academic departments get additional faculty or instructor salary for teaching students from outside their department – essentially a question of where tuition revenue is spent. Departmental course content is tailored to the intended student audience.  If a course is popular across the university but does not have applicability or appeal to the students within that faculty or instructor’s department, it can be difficult to justify spending time on it because most instructors or faculty are contracted to specific departments or academic unit budgets. However, a course with broad appeal could be taught outside of our contracted time, such as during winter or summer sessions, or potentially during the academic year as “overload teaching” which is above the number of credits outlined in our contact. This usually pays on top of the 9 or 12 month salaried contracts of instructors, but is restricted by the lack of free time that most faculty face.

Theory or approach to teaching

After settling on what should be taught, how, then, does a department decide how a class should be taught or constructed? How broad or specific should the information be, and how will the assignments or course requirements assess what students have learned? How will skills be taught? Broadly, this is called pedagogy: the method and practice of teaching, and is something which many faculty find themselves responsible for knowing even if we have not gotten an opportunity to develop our pedagogy in previous jobs. Prior to being an assistant professor at UMaine, I taught several different courses, including ones with pre-set materials that I re-hashed and presented in my own way, and ones with materials that I collected and decided entirely how to present (taught as electives). It wasn’t until that I was a long-term member of an academic department that I was able to participate in setting the direction of departmental courses, and to consider what we teach and how.  As part of my application to my current position, and my tenure packet (application to get a forever contract for my job), I am required to explain my teaching philosophy and how I put those ideas into practice in the classroom. I have previously shared some of those working documents.

As an example: it’s important to learn about how microbes affect animal health. Do I need to spend all my time lecturing to provide that info, or is there another format of information sharing I can use? I certainly need to lecture some, to introduce new topics or walk students through reading complicated graphs. But, it’s important that I also teach students how to find this information and assess it on their own, because they will be doing that for the rest of their life after they leave the classroom. Thus, I need to design my class materials and timeline to provide information and empower students to develop those same skills that I learned to get where I am: reading graphs, considering multiple and conflicting study results, forming questions and how to go about finding the answer. I might start a class with some lecture, followed by an assignment where students have to identity a question they have about microbiomes, then write down the expertise or people needed to find the answer from multiple perspectives, and finally outline what they thought that team could get done in one year.

Getting courses approved

There are many steps in the course approval process and, naturally, plenty of paperwork. In addition to a draft syllabus, a course proposal form is required which provides the logistical details (how many credits, lab or lecture, in person or online, and more), and describes the goals and scope of the content (introductory or experienced level), intended audience (students in which departments and which year of study), and how it will provide necessary skills or info to them. Importantly, the proposal form must describe how the new course will complement current courses that are offered at the University. Being able to show that there is a demand for this specific course, or that it is needed for professional development of the students, will support the course proposal during the approval process. This last part requires the person proposing the course to communicate with instructors of similar classes who might have students that will want to take this class. Are there aspects that you could include in your new course to make this more relevant to them, or to connect this new class to existing classes?

avs-254-new-course-proposal-2019Download

Once the proposal form is complete, it gets sent to the unit or departmental faculty committee for discussion, and may be returned for revisions. This committee might be made up of senior faculty in the department, or all the faculty if it is a small department. Not only can other faculty help improve the courses, but the time you spend teaching a course is time you can’t spend teaching other things that the department needs. So, your colleagues need assess whether this course is a good use of time and effort.

If the course is approved by the department, the proposal goes to the college curriculum committee which is made up of faculty from multiple different but related departments (for example, one from each department in the College of Natural Sciences, Forestry, and Agriculture). Often, faculty sitting on this committee are Undergraduate Coordinators in their own department, and have a lot of input into the scope of what undergraduates study.  After that committee, the proposal then goes on to the university curriculum committee to make sure it complies with university-wide standards and formatting. There are different forms and committees for undergraduate or graduate courses, and if you create a cross-listed course which can be taken by senior undergraduates and graduates, you’ll need to submit both forms and talk to both committee sets.

If a course is approved by the university, it will be assigned a number and will start appearing on the course catalogue. If the course is going to be required for students, though, it will usually be offered as an elective for the first year or even two before it is required for incoming students (current students can take it as an elective). Courses may also fulfil multiple requirements at once. For example, my AVS 254 Intro to Animal Microbiomes is required core subject material for AVS students, but also fills a university general education requirement to take a course that includes population and environment-scale information. In learning about the microbial communities, students also learn about microbial transmission between individuals, lifestyle choices and impact on host microbes, and interaction with the environment and affect on host microbes.

Matching faculty expectations to student experiences

An important consideration for course design is matching faculty expectations with student experiences. For example, the course materials which faculty see describe the course, but those faculty do not attend the course and experience how that information is shared. Thus, faculty may think that students are receiving information or skills, but the way that it is presented is not approachable or pertinent for students and they are unable to reuse what was presented in the course. Even faculty did audit a whole undergraduate course, we don’t have the same perspective that students do in that we might already be familiar with the material and we would not be able to identify where a lecture left out general information that would be critical for someone who is new to this. The student perspective is also driven by their need to do well in the course, not only by receiving a high grade but also by absorbing as much information which can help them in other classes or in their future career. Thus, aspects of the course which students think are interesting or important are not necessarily the same aspects that faculty identify as important.

Aligning the faculty and the student perspectives requires regular assessment of the course to make sure it is providing the necessary training and information to students. Often this assessment takes the form of faculty input and opinions, or changing needs of post-graduation industry career needs. It also relies on end of the semester evaluations of student performance (grades), and student feedback and evaluation of the courses. Student feedback can be unreliable when feedback on the course is preoccupied with comments which come from a place of personal bias or outright hostility. And, most course evaluations don’t provide enough granularity in the questions to thoroughly assess student perspectives on different aspects of the course, forcing students to give overall ratings. However, student feedback can be valuable when combined with other sources of information or asks more detailed questions.

To that end, Samantha Coombs, an AVS senior undergraduate researcher and I are designing surveys to gather student and faculty mentor perspectives for the UMaine AVS program Capstone Experiences courses, AVS 401 and 402. These courses are required for undergraduates to take to earn their bachelor’s degree, and require students to propose, conduct, and present results on research – often for the first time in their time at UMaine. If this wasn’t stressful enough, students typically work on projects which are part of faculty’s research portfolio,  and both students and faculty can be impacted by mismatches in expectations versus the reality of those collaborations. While we won’t be fully sharing the results of those surveys, we will be sharing summaries, and how the responses impacted future course materials in AVS 401 – the course in which students are first launched into research.

Improving the Curriculum for Future AVS 401 Undergraduates

Authors: Samantha Coombs and Dr. Sue Ishaq

Affiliations: School of Food and Agriculture at University of Maine, Orono

Keywords: Capstone, AVS 401, Undergraduates, Faculty, Stress, Mentor, Curriculum

Abstract

AVS undergraduates are not prepared to complete the requirements of AVS 401, before taking the course. In the AVS degree program, it is expected that undergraduates will gain knowledge, experience, and ideas to create a research project of their own. In many cases, AVS undergraduates are completing their capstones with never having performed a research project on their own. This is stress-inducing due to undergraduates having to learn both how to complete a research project, and how to write and complete a proposal. Undergraduates are given the choice to join a research project guided by a faculty mentor, but this leads to striving to meet expectations. Others struggle due to not knowing what project or path to go down. Each student needs a different situation that best fits their needs; this project will assist in trying to create a one-size-fits-all curriculum. The question I want to figure out is, can we adjust the curriculum in AVS 401 to meet the requirements of all AVS undergraduates for them to succeed in their capstone research? I hypothesize that we can create a curriculum that meets the requirements of undergraduates by surveying both faculty and undergraduates on their different expectations and experiences. Methods of research that will be conducted are, surveying AVS and other degree professors, surveying undergraduates who have taken AVS 401, reading syllabi, and reading scientific articles. The impact that this research will have is to create a class that is a one-size-fits-all for AVS 401 undergraduates. The curriculum will be adjusted due to the responses from both parties. The results will be a class that teaches undergraduates what they need to know to improve: the quality, efficiency, and reduce the stress of capstone projects.

Rumening through camel microbes, by Myra Arshad

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Written by Myra Arshad

Myra Arshad

Did you know that camels have three stomach chambers or that they have to throw up their own food in order to digest their food properly? Have you felt excluded from science spaces before? Then this blog post is for you!

Allow me to introduce myself. 

My name is Myra, and I am a rising senior at SUNY Stony Brook University, where my major is Ecosystems and Human Impact, with a biology minor. In a nutshell, my major is interdisciplinary with a focus on conservation and ecology within human societies. 

If I were to describe my college experience in one word I’d pick “surprises”. I never actually saw myself being a scientist in my middle and high school years. I found it hard to care about abstract concepts or theories that felt so far removed from humanity, particularly minority communities. But, during college I found myself falling in love with environmental studies, and along with it, the beautiful complexities that come with being human in our increasingly anthropogenic world. 

At UMaine, we focus on the One Health Initiative, which views the health of humans, animals, and the environment as interconnected. When COVID-19 caused everyone to go into lockdown, I was fortunate to find this farm was looking for crew members, with a focus on food security. While certainly not how I planned to spend the summer of 2020, farming for underserved communities is where I saw how impactful One Health was. Organic farmers commonly use plastic mulch as a popular alternative to pesticides for weed suppression. At my home institution, I lead a project on the impacts of microplastics on earthworm health, an Ecotoxicology lab (students of the lab affectionately gave it the nickname “the Worm lab”).  We use earthworm health as an indicator of soil health, which in turn is crucial for crop flourishment. The Worm Lab and farming emboldened me to pursue science and, ergo, look for this REU! 

At UMaine, I am a member of the Ishaq Lab where I work on the camel metagenome project. Basically, scientists in Egypt raised camels on different diets, then used samples from their feces to sequence their microbial genome. These microbes live in the camel rumen (part of the camel stomach), and help the camel digest their food. What I do with Dr. Ishaq’s lab is, I perform data analysis on these sequences to see how the microbial gene profile changes with different diets. Camels are essential for transportation and food for the communities that rely on them, so finding the most efficient feed for them is important. Camels also release methane depending on their diet so it’s possible humans could control methane production of camels through their diet. 

Being a part of the REU ANEW program for 2021 definitely has been an interesting experience, since it is the first time this program has been conducted virtually. Even though I would have loved to have seen everyone in person and spent time in lovely Orono, Maine, I’m glad for the research opportunity as it has further solidified my love of research and the One Health initiative.

Myra’s poster for the REU Research Symposium, virtual, Aug 13, 2021.