Every year, The University of Maine releases a summary report of the research efforts of its faculty, staff, and students. I was pleased to discover that the work that Yanyan Li and I have been doing on broccoli sprouts and gut microbes was featured in the report! A screenshot of the story is below, but you can read the story and the entire 2022 UMaine research report here.
The Microbes and Social Equity working group has published its second collaborative paper together, led by Dr. Jake Robinson and featuring 25 other MSE group researchers in various fields related to microbiomes, social equity, and ecosystems. In developing this paper, we had many conversations about what had been accomplished in research related to microbial exposure, as well as what had yet to be done. We provide some background information as context, and spend the majority of the paper outlining twenty of the most poignant research directions. There are so many questions yet to be answered about the way the microbial communities interact with human lives, and how our lives impact them back. In our enthusiasm for the topics, we could have endlessly chatted about research, such that we decided to limit ourselves to twenty questions. We hope that this piece becomes a source for inspiration for others who continue this conversation and future research in these areas.
You can find a link below to read the full article, and links to the authors’ twitter feeds if you’d like to check them out on social media. You’ll be able to hear more about this publication in an upcoming seminar from Jake, as part of the 2022 MSE speaker series, which is open to all and free to attend over zoom.
Robinson, J.M., Redvers, N., Camargo, A., Bosch, C.A., Breed, M.F., Brenner, L.A., Carney, M.A., Chauhan, A., Dasari, M., Dietz, L.G., Friedman, M., Grieneisen, L., Hoisington, A.J., Horve, P.F., Hunter, A., Jech, S., Jorgensen, A., Lowry, C.A., Man, I., Mhuireach, G., Navarro-Pérez, E., Ritchie, E.G., Stewart, J.D., Watkins, H., Weinstein, P., and Ishaq, S.L. 2022. Twenty important research questions in microbial exposure and social equity. mSystems 7(1): e01240-21. Special Series: Social Equity as a Means of Resolving Disparities in Microbial Exposure
Social and political policy, human activities, and environmental change affect the ways in which microbial communities assemble and interact with people. These factors determine how different social groups are exposed to beneficial and/or harmful microorganisms, meaning microbial exposure has an important socioecological justice context. Therefore, greater consideration of microbial exposure and social equity in research, planning, and policy is imperative. Here, we identify 20 research questions considered fundamentally important to promoting equitable exposure to beneficial microorganisms, along with safeguarding resilient societies and ecosystems. The 20 research questions we identified span seven broad themes, including the following: (i) sociocultural interactions; (ii) Indigenous community health and well-being; (iii) humans, urban ecosystems, and environmental processes; (iv) human psychology and mental health; (v) microbiomes and infectious diseases; (vi) human health and food security; and (vii) microbiome-related planning, policy, and outreach. Our goal was to summarize this growing field and to stimulate impactful research avenues while providing focus for funders and policymakers.
One aspect of research which requires substantial training, adherence, and reflection for researchers, yet gets almost no public attention, is the rules and regulations on the responsible conduct of research. In this piece I focus on the US, but many countries have ethical guidelines of their own. This piece is meant as a reflection of how far science and society have come, and while ethics in science are only as good as the scientist, I wanted to share the stringent approval and review processes that modern research must go through prior to completing any work, to ensure safety and respect for all persons and animals. Thus, please don’t read the first section and run off thinking that researchers are monsters – it is there to give you an understanding of where we ae now.
Bias and the misuse of research
If you’ve ever read “The immortal life of Henrietta Lacks”, by Rebecca Skloot, you are familiar with a high -profile case which took decades to uncover. The book examines the case of a woman, Henrietta Lacks, with cervical cancer whose cells have revolutionized medicine and research. However, doctors didn’t ask for her permission to use those cancer cells, she didn’t know they were being taken, her family didn’t know they were being used extensively in research labs around the globe, and even decades later they have not benefited from the billions of dollars of research and development profits that came about because of her cells.
History is littered with examples of cruel or nonconsensual research going back hundreds of years. Most of those involve intensive research on humans or animals without their knowledge or their consent, other examples include disregard for safety or privacy. Even decisions which appear benign but are still unethical prevent people from benefitting from their own contributions to research.
However, nearly all of these historical examples involving human subjects research are rooted in racism, sexism, and/or anti-religious or religion/ethnic cleansing. Historically and today, science has often been intentionally misconstrued to perpetuate social constructs of superiority/inferiority. Science is only a tool, and while these examples can be blamed on individuals choosing science to be the tool of their ill-intent, the historical lack of ethical guidelines, constraints, or consequences belies the failure of society to ensure equality and respect to all persons. There are numerous resources (for example, here and here) which examine these past offenses in detail, and reflect on how they led to the ethical guidelines we have in place today.
In addition to the obvious harm it could cause, not incorporating ethics into research contributes to Institutional Betrayal. This concept was coined by psychologist Dr. Jennifer Freyd, and describes the harm caused or allowed to happen by an institution, which causes psychological damage because you expect the institution to protect you. Collectively, unethical research leads to a distrust of science, researchers, and medical professionals, and can lead to science denialism.
One of the challenges to understanding ethics in scientific research is that our ethics reflect our values as a society and those values and laws change over time. You only have to read the news to see that we all have different ideas about what is acceptable to do to someone else. We should not think of everything that is permissible as also acceptable: just because you can do something, doesn’t mean you should do it. And, you can still take advantage of someone even if you are not physically harming them. Thus, ethical standards inform what we are able to research, but also why we are doing it, and how, as there may be less invasive methods available.
Importantly, ethical standards takes power away from the researcher and puts it into more objective hands. If a researcher wants to do a project, and millions of dollars of research funding, 20 research staff, and their careers are all based on the research succeeding, that puts a lot of bias in all of their thoughts and actions. Ethical review helps ensure that researchers are making good decisions before, during, and after the research.
Perception of authority and power dynamics
Americans have historically distrusted science, and this has always been encouraged by various social and political entities. This external influence on our perception of science has intensified in recent years, which has become dramatically clear in the way that people have responded to the pandemic. However, generally when people look at photos of researchers, scientists, or doctors, and they respond that they have some level of trust in them. This trust, of course, varies by gender and race and is rooted in how certain demographics have been taken advantage of previously.
There is a term called perception of authority, which can be used to describe how people ascribe authority to researchers, scientists, and doctors simply based on visual cues (like wearing a white coat). However, this perception can be incorrectly attributed to people who appear to be in that same category but are in fact not trustworthy or knowledgeable about the topics they claim to be experts in, for example, some TV personalities.
Ethical standards and review prevent researchers from intentionally or unintentionally taking advantage of participants’ willingness to say “yes” based on their perception of you being an authority, whether or not you really are. That is just one example of a power dynamic.
Research sets up a power dynamic, which is a relationship wherein one person has more power, authority, or control over another person. In research, there are a lot of ways in which that can be set up.
In addition to perception of authority, there is a perception of luck, in which participants assume they will be in the placebo group (the control group which receives no treatment to make sure the effects you see are because of the treatment and not just from the excitement of being in a research study) and dismiss concerns about potential risks. Financial incentive for participating may recruit people that really need that money and feel pressured to be int he study regardless of the risks. There is also the hope of a cure. For medical research involving obscure or rare diseases, studies may use developmental treatments and by necessity must recruit participants who suffer from this particular problem. You might be more like to participate if you assume that the treatment will cure you, or if you don’t understand that it is equally likely that you could be in a placebo group as in the treatment group. There are also people that feel pressured to consent because they have less social impact and power and feel that they can’t say ‘no’ to participation, by refusing to enroll or by withdrawing from the study at any time. Ethical regulations specifically include prisoners, children, pregnant people, and anyone without the ability to make an informed decision under special protections against power dynamics, but ethical review boards will help you identify other situations or demographics and how to lessen those power differentials.
In addition, having a study approval that rests with a committee who are in no way involved with the research can help reduce bias or harm. These standards may require researchers to be more creative in order to do less harm and find a better way to conduct that research, either by using alternative methods or fewer participants. Ethical review boards also ensure that researchers get the most out of the study, such that if some harm, even just some inconvenience, is being done to someone (human or animal), the benefits from the study are worth the cost and that judgment call is made by someone with no stake in the research. Review also ensures that the study is designed to collect as much info as possible so that it does not have be repeated.
Ethical standards also require researchers to obtain informed consent from your human participants. This includes what will be done to them during the study, what information or samples will be collected, what information (including methods) will be obtained from these samples, and what will be done with their samples or information in the future. Finally, ethical standards creates accountability for researchers’ actions by creating a paper trail, setting up oversight on the project, and creating consequences for failure to comply with regulations.
The logistics of ethics
How do we add ethical principles to our research? To summarize, you want to minimize harm to participants, be transparent about your activities and keep human participants well informed, keep excellent records and document all communications and information you share with human participants, always get Institutional approval before conducting research or collecting samples or information, and try to reduce the power dynamic by making yourself accountable for your actions. There are many guiding principles available, including some listed here provided by the NIH:
- Social and clinical value
- Scientific validity
- Fair subject selection
- Favorable risk-benefit ratio
- Independent review
- Informed consent
- Respect for potential and enrolled subjects
Institutional Animal Care and Use Committees (IACUCs)
If research involves live, vertebrate animals in some way and has a hands-on or disruptive aspect, approval from the Institutional Animal Care and Use Committee (IACUC) is required prior to starting the work. These regulations and guidelines stem from animal welfare laws and guidelines.
You should always consult with your IACUC board about your project before you have made preparations or started any work, as they should be kept apprised of research for reporting purposes and are the ones to verify if you do or do not need a formal approval. You typically don’t need formal approval if you are only observing animals and not interfering with them in any way or holding them captive, if you are collecting discarded animal products (like feathers), or if you are collecting tissue from carcasses. Keep in mind, you will need institutional biosafety approval to conduct this research if there is a specific infectious disease concern, and you need approval from your state fish and wildlife department if you are collecting samples from wild animals (even more so if the animal has a protected status). If you will be transporting biological material across state or national borders, there is another layer of training and approval before you can begin.
Each institution which performs animal research in the US is required to form at least a 5-member committee, which has to include the attending veterinarian at the institution with experience and training in the care and use of laboratory (and livestock) animals, one member from the local community, a practicing scientist experienced in research involving animals, a non-scientist, and at least one more member of any kind (usually another practicing scientist at the university).
In addition to applying to IACUC for approval for your study, you’ll need to document that everyone on the project has completed relevant training on responsible research conduct, animal handling, and the procedures you will be using. Some of that training is administered by your institution, but much of it will be performed through the Collaborative Institutional Training Initiative (CITI), which provides standardized information and training.
Institutional Review Boards (IRBs)
If research involves humans in some way, including surveys, approval is required from the Institutional Review Board (IRB) prior to starting the work. Even if your project ultimately does not require approval, you should always contact your IRB first, to let them know what you intend, and get their informal approval that you don’t need formal approval from the committee to do your work.
The members of the IRB committee may not have a personal, professional, or financial conflict of interest, and the federal code of regulations stipulates many guidelines about membership:
“Each IRB shall have at least five members, with varying backgrounds to promote complete and adequate review of research activities commonly conducted by the institution. The IRB shall be sufficiently qualified through the experience and expertise of its members, and the diversity of the members, including consideration of race, gender, cultural backgrounds, and sensitivity to such issues as community attitudes, to promote respect for its advice and counsel in safeguarding the rights and welfare of human subjects. In addition to possessing the professional competence necessary to review the specific research activities, the IRB shall be able to ascertain the acceptability of proposed research in terms of institutional commitments and regulations, applicable law, and standards of professional conduct and practice. * * * The IRB shall therefore include persons knowledgeable in these areas. If an IRB regularly reviews research that involves a vulnerable category of subjects, such as children, prisoners, pregnant women, or handicapped or mentally disabled persons, consideration shall be given to the inclusion of one or more individuals who are knowledgeable about and experienced in working with those subjects.”Code of Federal Regulations, Title 21, Volume 1, Revised as of April 1, 2020, CITE: 21CFR56.107
Generally speaking, you’ll need IRB approval (and training) if you intend to publish this work or share this information widely, if you are collecting sensitive information (such as health, finances, or anything which would put the safety and wellbeing of that person at risk if it were revealed), if you are collecting (biological) samples, if you are doing anything physically or psychologically invasive, or if you are working with vulnerable populations. If you will be transporting biological material across state or national borders, there is another layer of training and approval before you can begin.
There are a number of information-gathering activities that don’t require review and approval, most of which are student projects that are part of coursework. These include interviewing one person for a biography on non-sensitive information, or interviewing multiple people on non-sensitive topics (such as asking about their favorite animal), performing a literature review or information search on non-sensitive or de-identified information, or creating science curricula.
Biosafety and chemical regulations
In addition to regulations on working with biological study subjects, there are additional health and safety regulations if your work involves anything infectious or dangerous. Institutional biosafety and chemical safety review requires researchers to describe all protocols, sample types and relative risks, and all safety and containment procedures – from the protective gear you will wear, to your sterilization or detoxification procedures, to the equipment you are using that could cause aerosolization and spread. There are yearly chemical and biosafety inventory reviews, laboratory walk-through audits, training, reporting, and equipment maintenance records that all go along with this.
Like any good policy, responsible research is best accomplished when there are consequences and an institutional dedication to enforcement. Not only are applications and training required prior to performing the research, but there are facilities audits, reporting, and other regular check ins. Because there is no much to keep track of, review boards and enforcement are there to help researchers set up good practices and protocols ahead of time, help you stay in compliance, and correct problems before they exacerbate. Researchers who refuse to obtain permission prior to sample collection, who change their protocols without notifying review boards, who flaunt regulations, or who commit ethics violations will risk losing their funding, their job, and in severe cases, could face criminal investigations.
As has become a New Year’s Eve tradition, here is the Ishaq Lab’s Year in Review for 2020! In previous years, I remarked on difficult and delightful times alike, but 2020 has been a year full of intense loss for so many, and some have unfairly borne more of that heavy weight. In reflecting on whether to go ahead with the post for this year, I chose to do so and to include a tone of optimism and hope because, for the first time in the Ishaq Lab, I am not writing the story of me, I am writing the story of we. Even though we couldn’t all be together this year, the Ishaq Lab has tried to do our best to stay connected, and I have had the pleasure of watching my new lab team work together and grow as scientists. I am proud of how they have handled this year, and I wanted to share their triumphs.
2020 was the year for launching the first official projects of the Ishaq Lab, including a field project, a mouse project, and a handful of data analysis or microbial community projects.
Early in the year, students began joining the lab, and we had our very first lab meeting, featuring Adwoa Dankwa (UM Perry lab), Alex Fahey (in the office with me), Tindall Ouverson (MSU, Menalled/Seipel lab), and Johanna Holman. Ironically, we had our first lab meeting over Zoom to facilitate students in multiple geographic areas, not suspecting we would only have virtual lab meetings this year.
The first field project was a literal one – a soil project! Because of the pandemic response in the spring and early summer, laboratory work was reduced until we could do so safely in enclosed spaces. But, we were able to launch a field project because the samples could be collected and processed by one person alone over the summer. Undergrad Nick Hershbine, who is majoring in Ecology and Environmental Sciences, has been investigating the microbial community in blueberry soil from farms around Maine. This is part of a larger project led by Dr. Lily Calderwood, and is supported by the Wild Blueberry Commission of Maine (“Exploration of Soil Microbiota in Wild Blueberry Soils“). Nick is in the process of data analysis and interpretation, and we hope to write up the preliminary results over the winter.
The Ishaq Lab also launched its first mouse project! This is my first time managing mice, and luckily I have expert collaborators at Husson University and a stellar grad student taking the lead on those portions. I’ll be overseeing the microbial ecology aspects, done by master’s student Johanna Holman for her graduate work. Joe Balkan, a Biology undergrad at Tufts University, has been reviewing previous literature for culturing protocols, and will be joining us for two weeks over break to help with some bacterial work. Undergrad Evan Warburton, who started in the fall semester, will pick up that microbiology work from Joe at the beginning of the spring semester.
The Ishaq Lab also had its first student presentation this year, by master’s student Sarah Hosler giving a graduate seminar on her proposed research for her degree, which involves host-microbial interactions in ruminants. The first portion of laboratory work for her project will take place starting in winter break. We’re not ready to share any details, but first we will be trying out some new methodology, as well as recreating some older methodology which has fallen out of fashion.
As part of that first step, Sarah will be assisting with the Capstone project of undergrad Emily Pierce, who was awarded a UMaine CUGR undergrad fellowship to fund her work this spring. Emily will be investigating host-microbe interactions during Cryptosporidium parvum infections, something which routinely devastates newborn livestock. We had anticipated running this experiment last summer, but postponed it for safety. Emily and master’s of professional studies Alex Fahey have made good use of that delay, however, and have been spending the time reading scientific manuscripts, assembling experimental protocols, and designing their project. Alex does not need to complete a thesis for her degree, it’s more about assembling a variety of skills, so she has participated in a number of supportive activities this year.
Undergrad Jade Chin has been working on her Honor’s Thesis project, the scope of which has had to nimbly pivot over the past year as we weren’t sure what we would be able to accomplish during the pandemic. For example, we spent two months waiting for DNA extraction kits to arrive due to supply shortages and the federal disruption of the postal service. Those kits are critical to the very first step of the experimental procedures and one we could not skip. Jade will defend her Honors thesis in spring 2021, including a written thesis, an oral presentation, and even a short interview with her thesis committee, although it will be less formal and less strenuous than a graduate-level defense.
Grace Lee, an undergrad at Bowdoin College, has been working on data analysis of microbial communities associated with lobster in aquaculture, which is part of a larger project by Drs. Debbie Bouchard, Jean MacRae, and Heather Hamlin. The dataset is a large and complicated one, though with an elegant experimental design. We anticipate writing up the results beginning this winter and continuing through the spring. Grace will be joined by an undergrad who I have been mentoring in my AVS 401 Capstone class, who will be contributing a literature review for the manuscript.
Three papers were published this year, which were all part of previous projects at former positions. This included the culmination of my post-doc work in the Menalled Lab from back in 2016, and one of the small projects I participated in while at BioBE from 2017 to mid 2019.
- Horve, P.F., Dietz, L., Ishaq, S.L., Kline, J., Fretz, M., Van Den Wymelenberg, K. 2020. Viable bacterial communities on hospital window components in patient rooms. PeerJ 8: e9580. Article.
- Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Dryland cropping systems, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities. mSphere 5:e00340-20. Article.
- Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Soil bacterial communities of wheat vary across the growing season and among dryland farming systems. Geoderma 358(15):113989. Article. This was accepted in 2019 but not officially published till 2020.
It’s very common to have a slump in publications when starting a new position, and particularly when that involves moving to a new institution and establishing a new lab group. Research can take awhile to gain momentum, especially when you need to recruit and train new lab members. Or, when those lab members have to pause their lab work for global public health reasons. The Ishaq lab isn’t worried, we’ll make up for it in 2021. With all the ongoing projects, we anticipate a handful of other papers being developed next year. I’ve also got four manuscripts that have been in review for months, a process which has also been (understandably) delayed because of the pandemic.
I taught three new classes this year; one that was new to me and two that I developed myself. In spring 2020, I taught a special topics version of my DNA sequencing data analysis class, which means that I got provisional approval to teach it as a one-off while I completed the full course approval. Because the data analysis class is cross-listed for undergraduate seniors and for graduate students, it needed to go through two different curricula approval processes, and curricula must be approved a certain amount of time before the first instance of the class. That class has now been formally approved as AVS 454/554. From the spring version, two scientific manuscripts are in review, and a third is in preparation while more data are added. We managed to achieve a lot in the spring class, considering halfway through the semester we switched to remote instruction only as the early throes of the pandemic descended.
The other two new classes I taught this fall, including the first part of the Animal and Veterinary Sciences Capstone Experience, AVS 401, which instructs students on writing and presenting research proposals and matches students with a research mentor to try and complete the project. It was particularly challenging to do that this fall, when many researchers still had their work on pause because of the pandemic. I’ll be continuing this class in the spring as AVS 402, in which students present what they’ve done. While only a few AVS students will pursue research as a career, they will all need to implement the scientific method and the ethos of research into their lives no matter where they end up. Being able to find, assess, and critique information are all critical skills which this Capstone Experience helps them to develop.
I taught AVS 254, Introduction to Animal Microbiomes. I’ve previously taught some of this material, but to very different student audiences, which required a lot of course development on the fly over the semester. Even with the previous material, I still needed to revise all my previous lectures to adapt to a new lecture length, add new ones to make up about half the semester, and, as our understanding of host-associated microbiomes evolves over time, the course materials needed to be updated (annually) to present up-to-date knowledge. The last lecture of the semester was a compiled video of ‘science journeys‘, featuring researchers in host-associated microbiology sharing what they work on and how they got here. You can watch the video, too!
I also spent a lot of time this fall curating the Teaching Statement portion of my tenure packet, some of which I shared as a series of posts this fall. Next spring I will have my third-year review, which will be the first official hurdle and where I get more substantive feedback from my peer committee about the trajectory of my teaching, research, and outreach as I develop my packet to apply for tenure in ~ year 5. In 2021, I have a planned blog post describing the history and process of tenure, and I will likely share other portions of my tenure packet, such as my research statement.
Presentations from my couch
As I recently posted, 2020 has been The Year of The Virtual Conference. Many conference in spring and summer of 2020 were outright cancelled, but some managed to revise their format and be held virtually later in the year. This was achieved with a combination of live-streaming and pre-recorded content, all of which became on-demand during the conference. Viewers could ask questions through a chat function, or by posting questions directly to the presentation page. While early attempts to host large virtual meetings with researchers in multiple time zones faced a steep learning curve, overall, I think many people realized the potential provided by a virtual platform. For example, without travel costs, more students and early career researchers could afford to attend, and researchers with family care, health, or other constraints could participate on their own time.
Seven of the eight planned scientific presentations of my work took place in 2020, listed here with some links to video content.
Similarly, seven of the eight planned public presentations took place, with some links to video content in the list below:
- University of Maine Medicine seminar series (virtual), “A crash course in the gut microbiome” , Nov 6, 2020. pdf of slides with annotated comments: ishaq-ummed-gut-crash-course-20201106
- Genomes to Phenomes (G2P) group, University of Maine. Co-hosted a session with grad student Alice Hotopp, on gut microbes and survival of reintroduced animals. Oct 30, 2020.
- University of Maine Cooperative Extension Oxford County 4-H Teen Science Cafe (virtual), “Gut microbes on the farm”, Oct 15, 2020.
- BioME (Bioscience Association of Maine) Virtual Coffee Hour, “What is a microbiome and where can I get one?” Oct 14, 2020. I introduced myself and my research to 65 participants, who are biomedical professionals and state representatives in Maine.
- University of Maine Cooperative Extension Oxford County 4-H Jamboree (virtual), “Gut microbes on the farm”, Aug 13, 2020. Video.
- Invited to lead Journal Club with the Fogler Library, August 4, 2020. led a 1 hour discussion on gut microbes and survival of reintroduced animals.
- Albright College Science Research Institute summer program 2020, which engages grades 5-12 in research. “A crash course in the gut microbiome”, virtual presentation, Aug 4, 2020.
I’ve also been endeavoring to promote the AVS Capstone Experience projects, in part by sharing student-written project summaries on social media and UMaine news outlets. I will do something similar at the end of the spring 2021 semester when projects are complete. And, the online conferences have gotten me thinking about how to create an on-demand virtual symposium that is open to the public…
I published 45 posts this year, including this one, and was much chattier this year with over 26,000 words total. The most popular post this year was What is academic Outreach/Extension, a sleeper post from 2017 which finally ended the popularity reign of Work-Life Balance: What Do Professors Do?. A number of posts were tied for the least popular this year with one view each, but at the bottom of that possibly-arbitrary list, was A collaborative project got published on the biogeography of the calf digestive tract!, a publication announcement from 2018.
My site had its most popular year, with just over 5,000 visitors taking >8,250 views from 112 countries, as shown in the image below. This November had a record number of visitors, with >1,100! In total, my site has had >15,200 visitors and just under 24,000 views since January 2016, more than I had imagined possible when I began. The website visitors are joined by 64 wordpress followers, 100 on Instagram, 113 on Facebook, nearly 1200 on Twitter, and 0 on Tumblr, which I set up because wordpress will auto-reblog to there, just in case anyone still uses Tumblr.
I picked up a new hobby this year – axe throwing! I tried it at an axe bar last winter and instantly took a shine to it. We made wood targets at home and bought a few throwing axes, and while I haven’t become the maverick I had hoped, it is a lot of fun. I’ve also picked up an arguably more useful skill, basic electrical work to change outlets and light switches! We’ve been slowly updating and renovating our house, and I’m looking forward to learning drywalling and flooring next near.
2021 is anticipated to be an exciting year, and will be a combination of wrapping up current projects so some of my students can graduate, as well as progressing the graduate work of Johanna and Sarah. In my “free time”, I’ll continue to fine-tune my curricula, and it’ll be back to the writing table as I revise the research proposals that I submitted this year which were not awarded funding. Of the twelve proposals I submitted in 2020, two were awarded, one is already revised and back in review, at least two will be revised and resubmitted, and at least two new ones are planned.
I’ll be part of my first graduate thesis defense as part of the committee, as Tindall Ouverson is expected to defend her master’s in 2021 from Montana State University. Tindall’s first paper on soil bacteria in agricultural fields is currently in review, and the data analysis for two more (one of which is not on soil microbes) is underway.
I’ll also be leading the committee for Jade’s Honors thesis defense in March. Alex won’t be giving a defense to finish her degree, but she’ll still be informally meeting her committee to reflect on her academic journey and if she’s prepared for a professional career. Johanna and Sarah will soon be inviting faculty to their committees, and next year I will be chairing those meetings.
I’ll be teaching the AVS 402 Capstone class for the first time, but as I already spent the fall semester with AVS seniors in AVS 401, it shouldn’t be any trouble. Just a LOT of revising papers and giving feedback. I’ll be teaching my DNA analysis class again, and will spend the next few weeks updating the materials from last spring when I taught the special topics version. I’ll also be compiling datasets for my students to work on, and hopefully, to turn into scientific manuscripts by the end of the semester.
A number of events developed by the Microbes and Social Equity working group will come to fruition in 2021, and I will finally be able to tell you about them in detail! Stay tuned for information on a speaker series running from February through April, a hybrid (virtual and in person) symposium in June, and a public announcement of a scientific journal special collection.
I’m also pleased to say that one of my cousins will be joining the website behind-the-scenes in 2021, to add alternative text to my website images to make them more inclusive. This and other work will serve as part of the requirement for science/service hours for membership to the Science National Honor Society! I’ll leave it to my cousin to make a formal introduction in a blog post on science accessibility, but welcome to the team!
See you next year!
Summer 2020 is…. here. This year has been unpredictable at best, but some things have stayed the same. For example, summer is one of my favorite seasons in which to work in science, because things calm down when the university is not in full session and I’m not facing a deluge of emails, meetings, and myriad small interactions that accumulate to eat up the day. I’ve been taking the time to prepare my laboratory, dive deep into scientific writing, and prepare for the increased teaching load I will have starting this fall.
You might think that the pandemic causing months of delayed or reduced labwork would have lightened my research load, but I’ve had more than enough to keep me occupied over this spring. Not only have I been submitting a few manuscripts for peer review at scientific journals from my time at the University of Oregon and Montana State University, but I have been working on some unanticipated manuscripts that coalesced this spring. This has included a project with a previous collaborator on diet and health, another based on soil microbial ecology led by master’s student Tindall Ouverson at MSU, and three more which were generated during my DNA sequence data analysis course that I taught this spring! Of these, I am lead author on two and contributing to the others at a variety of depths. Some require a great deal of my time, while others require only editing and review.
And then there were 10! I now have three University of Maine master’s students and 4 undergraduate students performing research in my lab, as well as three other graduate students from other labs who are affiliated with us (as in, I am on their committee). In addition to training them on scientific research theory, laboratory protocols, and data management and analysis, they are getting general training in scientific literature review and critique, scientific writing and presentation, and laboratory management.
Lab space renovations
I am preparing the second of two laboratory spaces for my research, and this space hasn’t been fully renovated in years. While still very functional, there have been a number of remodeling, refinishing, and reorganization steps which needed to be taken to get it in line for biosafety level II microbiology work.
I have been doing much of this work personally, because it’s cheaper, and I have experience in basic home renovations. And, I enjoy the opportunity to put my email inbox away and let my thoughts wander to scientific theory while I use power tools.
When it is ready, I’ll be starting the wet-lab research into gut microbiology and doing more culture work to supplement the genomics work. To aid in that research, I’ve been acquiring more nifty bits of equipment.
Course materials development
Over the spring, I piloted a new course as a special topics version, and I have just been approved to teach that as an official course starting in spring 2021! This summer, I have and will continue to revise my teaching materials from the spring version to prepare them for AVS 454-554 next year.
I’ll be teaching two courses starting in fall 2020, one on animal microbiomes and one on undergraduate research for animal science students. AVS 254, on animal microbiomes, is material I have taught at other institutions with a different course focus. For that course, I will be updating the course material, adding new lectures from scratch, and revising the formatting of powerpoints. I’ll also need to make some of it more accessible for asynchronous online learning, depending on how the semester is organized this fall. This means pre-recording the lectures, and putting more effort into the online learning software I have available.
The other course I am teaching is new to me, AVS 401 (and 402 each spring), the AVS Capstone experience. I’ll be teaching students how to write scientific proposals, research papers, and give scientific presentations, as well as guiding them through participation in research along with faculty mentors. For many students, it’ll be their first experience participating in research. This year, since many students are unable to participate in in-person research and labs have been closed, it’ll be extra challenging to come up with projects, but I have some creative ideas in mind.
Works in development
In addition the above objectives, I have a number of things in development which are not yet ready to be shared in detail. These includes new research collaborations, leading a team to organize a journal special collection, and leading a team to organize and host a (virtual) mini conference meeting in the fall!
Faculty positions and summer work
Now, as an assistant professor at the University of Maine, I’m on a 9-month contract. During the academic year, I devote 50% of my time to research-related activities, and 50% to teaching/advising/mentoring– related activities. I have the option of working in the summer, or taking it off unpaid. However, my summer salary is contingent on me being awarded research funds which will pay for the work, something which is not guaranteed in this funding climate. It is generally not advisable for pre-tenure faculty to spend summers idle, and in any case, I would inevitably have to perform work of some kind over the summer to keep pace with my workload.
I am lucky enough to have start-up funding which can pay up to 2 months of summer salary per year during my first 3 years; however, I am expensive: one month of my summer salary is the equivalent of 1 full-time undergraduate researcher for 3 months, or a sizable chunk of a research project. On the one hand, I want to value my time and effort, and being paid for summer research helps close the gender pay gap for salary and retirement contributions. On the other hand, I am also forced to consider how to get work done on a reduced budget, should federal funding not come through. After all, being awarded tenure is contingent on productivity.
In May, I was adamant about taking the entire month of July off, as 2019 and 2020 have been incredulously busy and stressful and I haven’t had a vacation since Feb 2019. Now, at the end of June, I’m not sure I could take off a full summer month and still output all of the above, plus be prepared for the challenges of teaching this fall. At least my working-from-home view is more or less a vacation-scape, and some surprise home renovations will at least keep me away from electronic screens for some of it.
As a new assistant professor at the University of Maine, 50% of my appointment is research. To establish my research, I started with curating a space to fulfill the needs of my work — “professional nesting”, if you will. I was allotted two adjacent rooms for my lab work, one as a microbial culturing space, and one for genomics work. I asked for and was granted separate spaces to reduce to likelihood of contamination sourced from my culturing space.
Prior to my arrival at the University of Maine, both lab spaces were set up to perform different research from what I do. This may not seem like it would interfere with my work, but the type of research you do will influence the machinery you need, each of which may have space or utilities requirements, as well as the flow of traffic through the room. To reduce the amount of time you spend moving around the room in search of elusive supplies, it’s best to curate work stations within the room. To that end, the Ishaq lab team spent several days re-arranging the large machinery and the table-top equipment, and then moving the supplies to the cabinets in corresponding locations. This change was most evident in the genomics room, that was previously used for human cell culture and biochemistry, shown below. At this time, I’m still working on updating the microbial culture room, which is larger and contained many more bits and pieces to organize.
Most research labs use extremely specialized equipment and machinery. Some of this was made available to me immediately; when research labs are discontinued, ownership of equipment and consumable materials reverts back to the researcher’s home department. I needed to purchase some of the more research-specific equipment, using some of the funds allotted to me for this purpose. Buying equipment can be stressful, because it can be incredibly expensive, and you want to be sure you selected the machine brand and range of capabilities for what you might want to do over the next 5 – 10 years, at least.
Finally, you need to stock your lab with reagents and researchers, but both of these have been temporarily put on hold as of March 2020, as we do our part to reduce the transmission of the Covid-19 virus. Whenever it is safe to do so, I look forward to completing the updates to my spaces and opening them up for collaborative work.
Notwithstanding the different reasons, 2019 has left us reeling, myself included. Early in the year, I was left scrambling to keep my science career going in the face of unsteady funding resources. Through a combination of collaboration, long hours of writing, a strong support network, a lot of luck, and a pragmatic demeanor, I landed a tenure-track faculty position and pulled off one of the best years of my career, to date. I deeply appreciate all of the concern, assistance, coffee, revisions in a timely manner, coffee, and support provided by so many individuals in the last year.
My momentous research activity of 2019 was joining the faculty of the University of Maine, Orono, School of Food and Agriculture as an Assistant Professor of Animal and Veterinary Sciences, beginning in September. In August, my partner, our patient dog, and I drove from the west coast to Maine on a 9-day adventure that would begin a new (and more permanent) phase of our life. From our education in Vermont, to my post-docs in Oregon, to my research faculty position in Oregon, to Maine, we loved the opportunity to live in various states, but are looking forward to having an address for longer than 2 years and more stable income forecasting.
The first few months of my faculty position have been busy! Notably, it’s involved a LOT of training, paperwork, getting acquainted with campus resources, and making connections. Some of these have involved seeking approval to take on graduate students, not just from my department, but students from other departmental programs that want their research to center around my lab’s specialties. UMaine strives to provide interdisciplinary opportunities for students, and as such, encourage multiple cooperating positions. In addition to being able to bring on grad students through the School of Food and Agriculture, I have just been approved as faculty in the Graduate School for Biomedical Sciences and Engineering, and have another cooperating position pending.
My work now spans three major research priorities. My lab will focus on the gut microbiome of livestock, and how microbes can be used to promote animal health and production. This will take shape in a variety of ways, including through global collaborations (more on those as they develop, but many of my previous rumen collaborations that began at Montana State are included in that). I’ll be taking on several graduate and undergraduate students in 2020 for these projects.
Through ongoing collaboration on projects led by Drs. Fabian Menalled and Tim Seipel at Montana State University, I’ll be participating in research to understand climate change and farming practices on wheat production and soil microbes. I am a graduate committee member for Tindall Ouverson, who is completing her master’s at MSU.
I’ll also be collaborating with researchers on microbes in the human gut. Through ongoing collaborations with researchers at the Institute for Health in the Built Environment (primarily those at BioBE) at the University of Oregon, I’ll be looking at infectious disease transmission and building design. And I’m currently developing new collaborations with researchers at Husson University, University of Maine, University of Vermont, and other institutions, which will investigate the interaction between diet, gut microbes, and human health. I’ll be taking on several graduate and undergraduate students in 2020 for these projects.
I published a record 10 papers this year! I don’t expect to achieve this again anytime soon: over the spring and summer I was only working half-time, and with the rest of my time I was doggedly writing up previous project results, overseeing undergraduate authors, and emailing co-authors for revisions. Writing or managing the writing of a manuscript takes a significant amount of work. Even when experiments or field trials are completed within days, weeks, or months, it may takes years to process, analyze, and measure the samples you collect, as well as complete the statistical analysis. You might encounter technical problems, or need to validate a method for use with your research. After all, much of what researchers do is trying new things, as there isn’t always a well-validated protocol to follow and you need to come up with something new. Thus, at least half of the publications from 2019 were wrapping up experiments that had occurred as far back as 2014!
Because of the time span, it meant I published on a variety of topics, from the effect of diet on rumen bacteria in sheep, to the effect of farming practices on bacteria in soil, to the effect of chemicals from vinyl floors on bacteria in dust. It meant a LOT of reading for me, to appraise and condense the relevant literature for each project: my citations list might contain up to 100 other papers!
Over the summer, I taught “Microbes and Social Equity” at The University of Oregon for the Clark Honors College. In just four weeks, the students, a few guest speakers, and I collectively wrote a paper to introduce the topic. We submitted it to the journal PloS Biology, and it was accepted for publication in their special call, Microbiomes Across Ecosystems. You can read it here. In the first month, it’s been viewed nearly 5,000 times!
I am developing new coursework for the University of Maine, including AVS 254 Introduction to Animal Microbiomes, which will be taught annually beginning in Fall 2020. This spring, I’ll be teaching a ‘special topics’ class, which will be the preliminary version of a class I am currently developing: DNA Sequence Data Analysis Lab, which will teach students the programming and analysis required to understand complex DNA sequence data, including amplicon, whole-genome, and metagenomics datasets. The special topics version is limited enrollment, and a way to beta-test the class before spending the significant amount of time required to develop a new course. I’ll be sharing more info about the classes as they develop.
Presentations and Travel
In May, I again presented my BioBE research to the Institute for Health in the Built Environment
Consortium meeting in Portland, OR. It was a quiet summer for me, but I did attend the Gordon Research Conference on Animal-Microbe Symbioses in Vermont, which showcased fascinating research on the ways that humans and animals interact with the microbes that inhabit our bodies. In October, I had a whirlwind week-long trip which involved giving a presentation in Monterrey, Mexico, then a different presentation in Reno, NV the following day, then heading to Bozeman, MT to catch up with collaborators and teach bioinformatics to Tindall. All of the meetings, seminars, and training was very valuable, but the best part, hands-down, was going to Matacanes canyon.
Over 2019, I gave more than ten (not all have been published) interviews on my research! This included a live radio interview, and two podcasts: all new experiences for me.
- “UMaine prof: Inequity is creating a gut microbe gap.” Mike Tipping and Ben Chin, Maine People’s Alliance. Dec 20, 2019.
- “Women in Science – Implicit Bias“. Ida Hardin. Dec 13, 2019.
- “Inequity takes a toll on your gut microbes, too.” Sue Ishaq, The Conversation, Dec 4, 2019.
- Picked up by The Telegraph, Alton, Illinois, and other agencies
- Included on UMaine news
- “All people have a right to healthy gut microbes.” Paige Jarreau and Signe Asberg, Lifeapps. Dec 3, 2019.
- “Rich People Have Access to Better Microbes Than Poor People, Researchers Say.” Becky Ferreira, Vice. Nov 26, 2019.
- “Microbiome is a Human Right.” Heather Smith, Sierra. Nov 26, 2019.
- “Life, liberty—and access to microbes?” Press release for Plos Biology. Nov 19, 2019.
- “Study finds season an important factor in soil microbe sampling.” Erin Miller, University of Maine. Nov 6, 2019.
- “cUriOus: Buildings Have Microbiomes, Too!” The Jefferson Exchange with Geoffrey Riley. Mar 8, 2019.
- ” The Great Indoors: Interior Ecology Under the Looking Glass.” Alex Notman, University of Oregon College of Design. Jan 14, 2019.
I published 30 posts this year, including this one, although with ~11,000 words total, I had less to talk about. I anticipate that will change when my lab gets rolling. The most popular post this year continues to be Work-Life Balance: What Do Professors Do?, self explanatory, and the least popular this year is I Accepted a New Position in Soil Microbiology and Agroeconomy!, which makes sense as it was an announcement from 2016 about a post-doc position I’d accepted.
My site had its most popular year, with >4,000 visitors taking >6,000 views, represented by 109 countries. In total, my site has had > 10,000 visitors and >15,000 views since Jan 2016
If you’ve read this far, you can probably guess how hectic my life has been this year. At the same time, it’s been gorgeously complex. I finally made it down to see Crater Lake in Oregon, went powder skiing in the Rockies in Utah, drove through the dramatic beauty of the Rockies in Alberta, made my first visit to Mexico and was immersed in the isolated beauty of a mountain canyon in Matacanes.
And… we bought our very first house!!
This Year in Review, I have the clearest idea of where my 2020 is heading. With a new lab and new classes, I’ll be happily well-occupied. I’ll be obtaining 3+ quotes to buy each piece of lab equipment (if it cost more that $6,000) and then waiting two months for it to arrive, troubleshooting R problems and revising scientific manuscripts written by first-time authors, I’ll be training my new brood of students in the lab, and I’ll be sharing my experiences here! Stay tuned!
Featured Image: Cookies from Mug Buddy Cookies
No one is sorry to say goodbye to 2018, yet it still seems like the 2018 Year in Review has arrived too soon. As usual, I’ve been keeping busy; you can find my reviews for 2017 and 2016 in the archives. For the first year in the
three years since I started this blog, I’m not starting a new job! I’ve been at BioBE for a year and a half, and it’s a relief to be in an academic position long enough to finish the projects you started (I’m only just starting to submit some manuscripts for work I did back in Montana).
Two papers of mine were published this year, including one on the bacteria along the GI tract of calves, one on the effect of dietary zinc on bacteria in sheep. A comprehensive culturing initiative of rumen microorganisms, called the Hungate 1000 Project, an international initiative to which I contributed data, was also published. That puts me up to 17 scientific articles, of which 9 are first-authored, as well as 5 scientific reviews. I have three manuscripts in review right now, and another five being prepared – 2019 will be a busy year.
I joined two journal editorial boards this year, PloS One and Applied and Environmental Microbiology. Both positions are as an Academic (or handling) Editor; I will oversee manuscript review by soliciting reviewers, assessing their recommendations, and interfacing with authors. In recent years, the gender discrepancy in science has received more attention, and some journals are making efforts towards increasing the number of female editors, reviewers, and contributors to reduce implicit bias in science publishing. I am pleased to be in a position where I can help change that!
I’ve been spending a lot of time writing grants and developing potential projects on microbiology and health in the built environment, many of which should be moving forward in 2019. I’ve also been spending time training the 9 undergraduate students I hired over the summer and fall to work at BioBE. In addition to microbiology and molecular biology laboratory skills, I have been training them on DNA sequence analysis and coding, scientific literature review, and science writing and communications.
This fall term, I taught Introduction to Mammalian Microbiomes for the University of Oregon Clark Honor’s College. I proposed this new course last year, and developed the curricula largely from scratch. I’d previously taught some of the subject material at Montana State University in Carl Yeoman and Seth Walk’s Host-Associated Microbiomes course; however in IMM I was teaching to non-science majors. The course went well, and I’ll be diving into it in detail with a full blog post in a few weeks. I proposed the course again for next year, as well as another new course; Microbiology of the Built Environment.
Presentations and travel
Early in the year, I gave two public talks on the gut microbiome for Oregon Museum of Science and Industry; one in Eugene and one in Portland. Both were a lot of fun, and I really enjoyed getting to share my work with the public.
In May, the research group I am part of (the Institute for Health in the Built Environment, comprising the Biology and the Built Environment Center, the Energy Studies in Buildings Laboratory, and Baker Lighting Lab) hosted a mini-conference in Portland in May; the Health and Energy Consortium 2018. I presented some results on how some home factors affect the bacteria community found indoors, as well as brainstormed research ideas with industry professionals and researchers.
At the end of the spring term, I also presented at the University of Oregon IDEAL Framework Showcase. Over the 2017/2018 academic year I served on the Implicit Bias working group, tasked with assessing the need for campus-wide training and making recommendations to the college.
In June, I attended the HOMEChem Open House at the UT Austin Test House, University of Texas at Austin’s J.J. Pickle Research Campus. I got to tour the amazing indoor chemistry labs there, and met with BioBE collaborators to discuss pilot projects exploring the link between indoor chemistry and indoor microbiology.
In July, I had a double header of back-to-back conferences, both of which I was attending for the first time. The first was Microbiology of Built Environment 2018 Gordon Research Conference in Biddeford, ME, followed by Indoor Air 2018 in Philadelphia, PA.
MoBE 2018 was an intensive meeting that brought together the top names and the rising stars of MoBE research. Gordon conferences are closed-session to encourage the presentation of unpublished data and ideas, and to facilitate discussion and theoretical contemplation. While in Biddeford, I had the opportunity to eat seafood, visit friends, and check out Mug Buddy Cookies!!
Immediately after MoBE, I flew to Philadelphia for the Indoor Air 2018 conference. I again presented some of the work I’ve been part of, exploring the effect of weatherization and lifestyle on bacteria indoors. I also found some incredible shoes.
Then, in August I went to Leipzig, Germany for the 17th International Society for Microbial Ecology (ISME17). Here as well, I presented some of the work I’ve been part of, and had the chance to revisit a city I haven’t been to in 5 years – since the last microbial ecology conference held here.
I spent a great deal of 2018 participating in activities for 500 Women Scientists. I am a Pod Coordinator for the Eugene Pod, and as such I meet regularly with other Coordinators to plan events. The majority of our 2018 events were Science Salons: science talks by local female researchers around a particular theme, with a hands-on activity to match, and a Q&A session about life as a (female) scientist. We heard about some awesome research, raised $1300 for local science non-profits, and learned how to be better community members by sharing personal stories about the triumphs and troughs of being a woman in science.
We also hosted a film screening of My Love Affair with the Brain, generously lent to 500WS by Luna Productions, followed by a panel discussion of women neuroscientists here in Eugene.
Along with two other Eugene Pod Coordinators, I wrote a small proposal which was funded, to coordinate workshops at UO: “Amplifying diverse voices: training and support for managing identity-based harassment in science communication”. Those workshops will take place in 2019.
This year, I acted as a judge for several robotics competitions and STEM design projects for local schools, I even dressed up as a giant spider to throw corn starch at campers. You know, for the kids.
I again participated in citizen science through Adventure Scientists, as part of their wood crews for the Timber Tracking 2018 campaign. Lee and I drove around a 20,000 sq mi section of southwestern Oregon to collect samples from big leaf maple trees at 10 locations which adhered to certain sampling parameters. Despite the large number of big leafs in Oregon, the sampling criteria made it difficult to find the perfect tree in an entire forest, and we logged a lot of mileage. Lee and I also volunteered for their Gallatin County Microplastics Initiative while we lived in Bozeman, MT.
I published 30 posts this year! The most popular post this year continues to be Work-Life Balance: What Do Professors Do?, self explanatory, and the least popular this year is Show Me the (Grant) Money, detailing the grant proposal writing process. Although, I was significantly less wordy this year as compared to other years.
As of today, my site received 4,447 view from 97 countries and 3,101 visitors in 2018. So far, I’ve published 109 posts, and received 6,147 visitors who viewed the site 9,481 times.
It’s easy to forget how many life events go by in a year, unless your social media is making you a video about them. But they were all important parts of my life and had some impact, however negligible, on my work. The one I’m most proud of was officiating the wedding of two dear friends, in Vermont.
I tried to spend more time on creative projects, including getting back into art after more-or-less tabling it for several years.
As usual, 2019 promises an abundance of opportunities. Already, I am planning out my conference schedule, seeking speakers for upcoming 500WS Science Salons, and writing, writing, writing. But through all of it, I will be trying to cultivate a more open, inclusive, and supportive work environment. In 2018, after more than a decade of trying to convince doctors that I should have agency over my own organs, I was finally approved for the hysterectomy that I’d wanted for so long, and the medical diagnostics to show that I’d actually needed it for probably just as long.
The surgery has dramatically improved my quality of life, and the scars are a constant reminder that you never know who is dealing with something in their life that isn’t visible to you, who is trying to pretend they aren’t in pain because they can’t afford to take time off to resolve their situation. At first, I kept the details to myself and I kept it off my professional social media. I did share, in exquisite detail, on my personal social media, and was flooded with similar stories from other women. It encouraged me to share a little more, after all, if I’d had surgery on a knee or a kidney I would talk about it openly, why not a uterus?
In a typical semester, one to two-thirds of the students that I teach or mentor will disclose that they experienced a serious life event, most often while at school. They may casually joke about how they couldn’t get time off or almost failed out that semester, or recall how receiving help saved them. I take my role as an educator, mentor, or supervisor seriously – the competition in academia forces students to work long or odd hours, to prioritize other things over study, to accept positions of low or no pay “for the experience”, or to accept professional relationships where they are not respected or may be taken advantage of. I have always tried to be a supportive mentor to students, but the higher up the ladder I climb the more important it is for me to set a good example for these students who will one day mentor people of their own.
In addition to listening to them, and having frank conversations, my response this year has been to get rid of student employee deadlines whenever possible. We are asked to do so much with our time in school, or in academia, but there are so many hours in the day. Sure, I routinely wish things were accomplished more promptly, but I have never once regretted not causing someone to have a breakdown. And constantly telling my students to take care of themselves first and work second reminds me to do the same, it benefits my work , and it’s made a certain furball very happy. Happy New Year!
This past year has easily produced the largest number of research topics I have been working on concurrently. In addition to publishing a paper on the rumen in cattle last September, I have been working on a paper on the rumen of yearling rams which is currently in preparation and due to be submitted to a scientific journal for review soon. I still have several small projects in development from my post-doc in the Yeoman lab, as well as a number of grad-student-led papers that are still pending, and was invited to contribute to a scientific review which is also in preparation.
I’ve been working through the large dataset of soil samples from my post-doc in the Menalled lab. That large project has blossomed into four papers thus far, two of which I’m writing on the soil bacteria, and one of which I am co-authoring on the legacy effects of climate change. Those four are also due for submission to scientific journals for review soon. The Menalled lab just received a grant award from USDA AFRI NIFA, on which I am a (subaward) PI and to which I will be contributing soil bacterial community analysis.
The rumen and soil work over the past year has been entirely in my spare time, however, as my position in the Biology and the Built Environment Center has kept me delightful busy. I have been collaboratively processing a large and complex dataset on weatherization, home operation and lifestyle, indoor air quality, and microorganisms in dust, which I will be presenting at two (possibly three) conferences this summer. I have also been collaboratively writing grant proposals, and while those are still in development or pending review, they span everything from light, to chemistry, to plants and living machines, to hospitals, to social networks in buildings. I hope to further develop some of these collaborations with a short trip at the end of June to the University of Austin, Texas’ Test House.
In addition, I have been assisting in the planning, development, and launch of the University of Oregon’s Institute for Health in the Built Environment. The Institute will facilitate collaboration and information sharing between researchers and industry professionals, with the goal of researching, building, and promoting healthier built environments. The Institute just hosted its #BuildHealth2018 Consortium meeting in Portland, OR, at which I presented some of the results from that large weatherization study regarding indoor plants. The meeting was fantastic, and spurred in-depth discussion on problems facing industry professionals, innovative research goals, and a wealth of new possibilities.
In the past few months, I’ve spent a lot of my spare time helping to develop the Eugene Pod of 500 Women Scientists, an organization created to promote diversity, equity, and inclusion in science, and to promote education and interactive between scientists and the general public. We have focused on hosting monthly Science Salon events, four to date, to do just that. I presented at the first one, and have helped organize and MC the others. The Eugene Pod’s activities were just featured on the central 500 WS page, as Pod of the Week, and you can also follow our updates and events on our Facebook page.
While it has been a struggle to maintain regular contributions, I still maintain Give Me the Short Version, along with a few intrepid contributors, which summarizes scientific articles for easier consumption. This spring, I spent several days judging STEM and robotics competitions for several local Eugene middle and high schools, which has been a lot of fun. The student projects are enthusiastic and creative, and I appreciate the chance to assist in these programs in some small way.
I have continued to mentor UO students. The post-bac student from the BioBE lab that was learning bioinformatics with me, Mitch Rezzonico, was accepted to the University of Oregon’s Bioinformatics and Genomics Master’s Program! Mitch wrapped up his work this spring to prepare for the intensive program, and with his interest in health research, BioBE hopes to work with him again in the future. BioBE recently hired an undergraduate student for science communication, Mira Zimmerman. Mira has been making some upgrades to the BioBE and ESBL websites which will continue to be rolled out over the next few months. In addition, she will be helping me develop informative blog posts on the built environment, and helping to grow our information dissemination capabilities. Hiring a student as a science communicator was something I had been hoping to test out, and so far it’s been a smashing success.
My course proposal for “Introduction to Mammalian Microbiomes” was accepted by the University of Oregon Clark Honor’s College for the fall term!
In April, I gave a guest lecture to Mark Fretz’s Design the Unseen course at the University of Oregon, on the Indoor Microbiome. The class was populated by architecture students, who were learning about integrating health considerations into design strategies. As a final project, students design a brief field experiment or intervention strategy for a design assistance project with Portland firms. I assisted one group in designing a small experiment on natural daylighting in an office and the effect on E. coli growth on culture plates – more on those results soon!
Later that same day, I have a lecture at the Oregon Museum of Science and Industry in Portland, as part of their OMSI After Dark series which opens the museum after-hours to adults for hands-on activities and lectures. The lecture was on the gut microbiome, and I was able to present in the Planetarium!
Last June, I started a position as a Research Assistant Professor of Microbial Ecology at the Biology and the Built Environment Center at the University of Oregon. The BioBE Center is a collaborative, interdisciplinary research team investigating the built environment – the ecosystem that humans have created for themselves in buildings, vehicles, roadways, cities, etc. With my background in host-associated microbiology, I am concerned with how the built environment interacts with biology.
Humans shed microorganisms constantly – every itch, every cough, every minute. In fact, our buildings are littered with the biological material shed from our bodies and our microbiomes (1, 2, 3, 4). Pets (1, 2) and plants (1, 2) also contribute, and so does outdoor air (1, 2). In fact, the indoor environment is full of microorganisms.
In addition to knowing how our presence, our behaviors (ex. cleaning), and how we run our buildings (ex. ventilation) creates the indoor microbiome, I want to know how the indoor microbiome affects us back. Not only can “sick buildings” negatively affect air quality, but they can harbor more microorganisms, especially fungi, or pathogenic species which are detrimental to our health.
My first indoor microbiome data is one that I have inherited from an ongoing project on weatherization in homes, and hope to present some of that work at conferences this summer. Since June, a large amount of my time has gone into project development and grant writing, most of which is still pending, so stay tuned for details. It has involved read lots of articles, going to seminars, networking, and brainstorming with some brilliant researchers.
As research faculty, I am not required to teach, although I have the option to propose and teach courses by adjusting my percent effort (I would use the teaching salary to “buy back” some research salary). As I am not currently tenure-track, I am also limited in my ability to hire and formally mentor students. However, I have been teaching bioinformatics to a student who recently graduated with his bachelor’s and is pursuing a masters in bioinformatics later this year.
I’ve also been keeping up with my science outreach. I gave a presentation on my host-associated microbiome work, I marched, I volunteered for a few hours at Meet A Scientist day at the Eugene Science Center, and I’m hosting a Science Pub on “A crash course in the microbiome of the digestive tract” at Whirled Pies in Eugene this Thursday, February 8th!