Update: on the very last day of June, I received word that two more papers had been accepted for publication, bringing the tally to five in the month of June alone!
I’ve previously discussed how many researchers end up with partially-completed projects in their wake, and I’ve made a concerted effort in the last 6-ish months to get mine across the finish line. I have five new publications which were accepted in June alone, with one reviews and one manuscript currently in review, and another three manuscripts in preparation. On top of that, I have a number of publications that are looming in the second half of 2019.
Ishaq, S.L., Lachman, M.M., Wenner, B.A., Baeza, A., Butler, M., Gates, E., Olivo, S., Buono Geddes, J., Hatfield, P., Yeoman, C.J. 2019. Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed. PLoS ONE 14(6): e0215797. Article.
I’ve already done the blog post and project page for the ‘particle size’ paper, so I’ll move on.
Stenson, J., Ishaq, S.L., Laguerre, A., Loia, A., MacCrone, G., Mugabo, I., Northcutt, D., Riggio, M., Barbosa, A., Gall, E.T., Van Den Wymelenberg, K. 2019. Monitored Indoor Environmental Quality of a Mass Timber Office Building: A Case Study. Buildings 9:142. Article.
This was a case study on a newly (at the time of sample collection) constructed building in Portland, OR which was made using mass timber framing. Since building materials alter the sound, vibration, smell, and air quality of a building, the primary goals of the study were to evaluate occupant experience and indoor air quality. Dust samples were also collected to investigate the indoor bacterial community, as the effect of building materials on the whole microbial community indoors is unknown. For this project, I assisted with microbial sample processing and analysis, for which I taught Georgia MacCrone, an undergraduate Biology/Ecology junior at UO, bioinformatics and DNA sequence analysis.
Garcia-Mazcorro, J.F., Ishaq, S.L., Rodriguez-Herrera, M.V., Garcia-Hernandez, C.A., Kawas, J.R., Nagaraja, T.G. 2019. Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits. Animal. Accepted.
This review was a pleasure to work on. Last year, Dr. Jose Garcia-Mazcorro emailed me, as I am the corresponding author on a paper investigating protozoa and fungi in cows with acidosis. We corresponded about fungi in the rumen, probiotics, and diet, and Jose graciously invited me to contribute to the review. Last August, after having worked with Jose for months, we finally met in person in Leipzig, Germany at ISME. Since then, we’ve been discussion possible collaborations on diet, probiotics, and the gut microbiome.
Horve, P.F., Lloyd, S., Mhuireach, G.A., Dietz, L., Fretz, M., MacCrone, G., Van Den Wymelenberg, K., Ishaq, S.L. Building Upon Current Knowledge of Indoor Microbiology to Construct the Next Era of Research into Microorganisms, Health, and the Built Environment. Journal of Exposure Science and Environmental Epidemiology. Accepted.
Seipel, T., Ishaq, S.L., Menalled, F.D. Agroecosystem resilience is modified by management system via plant–soil feedbacks. Basic and Applied Ecology. Accepted.
And as a reminder, I’m a guest editor for the PLoS ” Microbiome Across Biological Systems” special issue call, which is accepting submissions into August!
I’m pleased to announce that the “particle size” project is officially published! I inherited this dataset of bacterial 16S rRNA sequences in 2015, while working for the Yeoman Lab. This collaborative project combined nutrition, animal production, and microbial ecology to look at the effect of diet particle size on lambs and their rumen bacteria. While small in size, the project was large in scope – despite everything we know about how different diet components encourage different microbial communities to survive in the digestive tract, we know practically nothing about how the size of the particles in that diet might contribute.
A lot of factors can be manipulated to help get the most out of one’s diet, including adjusting ingredients for water content, palatability, ease of chewing, and how easy the ingredients are to digest. For example, highly fibrous foods with larger particles/pieces require more chewing, as well as a longer time spent in the rumen digesting so that microorganisms have plenty of time to break the chemical bonds of large molecules. Smaller food particles can reduce the time and effort spent chewing, allow for more surface area on plant fibers for microorganisms to attach to and digest faster, and speed up the movement of food through the digestive tract. On the other hand, moving food too quickly could reduce the amount of time microorganisms can spend digesting, or time the ruminant can absorb nutrients across their GI tract lumen, or cause slow-growing microbial species to wash out.
Suzanne L. Ishaq1, Medora M. Lachman2, Benjamin A. Wenner3, Amy Baeza2, Molly Butler2, Emily Gates2, Sarah Olivo1, Julie Buono Geddes2, Patrick Hatfield2, Carl J. Yeoman2
Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America
Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America
Abstract
Diet composed of smaller particles can improve feed intake, digestibility, and animal growth or health, but in ruminant species can reduce rumination and buffering – the loss of which may inhibit fermentation and digestibility. However, the explicit effect of particle size on the rumen microbiota remains untested, despite their crucial role in digestion. We evaluated the effects of reduced particle size on rumen microbiota by feeding long-stem (loose) alfalfa hay compared to a ground and pelleted version of the same alfalfa in yearling sheep wethers during a two-week experimental period. In situ digestibility of the pelleted diet was greater at 48 h compared with loose hay; however, distribution of residual fecal particle sizes in sheep did not differ between the dietary treatments at any time point (day 7 or 14). Both average daily gain and feed efficiency were greater for the wethers consuming the pelleted diet. Observed bacterial richness was very low at the end of the adaptation period and increased over the course of the study, suggesting the rumen bacterial community was still in flux after two weeks of adaptation. The pelleted-hay diet group had a greater increase in bacterial richness, including common fibrolytic rumen inhabitants. The pelleted diet was positively associated with several Succiniclasticum, a Prevotella, and uncultured taxa in the Ruminococcaceae and Rickenellaceae families and Bacteroidales order. Pelleting an alfalfa hay diet for sheep does shift the rumen microbiome, though the interplay of diet particle size, retention and gastrointestinal transit time, microbial fermentative and hydrolytic activity, and host growth or health is still largely unexplored.
I’m excited to announce that I’ll be giving a presentation at the American Fisheries Society and The Wildlife Society 2019 Joint Annual Conference this September. I was invited to participate in a symposium: Utility of Microbiomes for Population Management. I’ll be returning to my roots and presenting on moose microbes. See you in Reno!
Abstract 36407 – “Moose Rumen Microbes and Their Relevance to Agriculture and Health”
Continuously in science, you find yourself with more ideas than you can possibly put into action, and more tasks on your daily to-do list than you can possibly complete in one day. Spring has been, predictably, busier than anticipated – so much so that I haven’t posted in over a month! Here are some of the highlights, and I hope to be posting more over the summer as papers get published and courses get taught.
Over the past few months I’ve been focusing on wrapping old projects; those large and small things that carry over even after a scientific position has run out of funds to pay you. Scientific research, and especially the interpretation and writing of results, takes a long time and often outlives short-term student, post-doc, or non-tenured faculty postings. Eventually everyone who collaborated on a project has moved on and it is increasingly more difficult to finalize and publish that work. And, most of the undergraduate students I’ve been working with at BioBE are graduating in June and need to finish their projects so they can cleanly begin the next phase of their life.
For the most part, wrapping these projects has involved writing up manuscripts, getting the authors to agree on a final draft (which can take weeks or years), and submitting it to a scientific journal for review. I currently have seven manuscripts in review; 4 scientific articles and 3 scientific reviews, some of which have been in review for months. And I still have at least four more papers that need to get finished and written up. I’m also a guest editor on a special call for papers through PloS One on the Microbiome Across Biological Systems, which to date has required communication and brainstorming from me but which will soon include quite a bit of editing and oversight.
February was generally absorbed by grant proposal writing, and it looks like May is shaping up similarly. Grant proposal writing is an arduous process requiring a lot of planning and coordination between contributing parties. The majority of proposals don’t get funded on their first round, which means you may sink a lot of time into developing something with a very delayed payoff. I am in the process of developing several highly-collaborative proposals which have been maturing into increasingly-finer wine.
Equity is not a term that’s typically associated with microbes, yet. The work this spring that I’ve been (happily) most absorbed in has been development of the summer course I’m teaching for the UO Clarks Honors College, Microbes and Social Equity. It’s only four weeks long, but will be four days a week, and I’m hoping to cover a number of different topics and coordinate several guest speakers, so there are a lot of lectures to make and emails to send.
Engagement on social media from me has been slim the past few months, but other science communications have been thriving. I gave a print interview with the UO College of Design and a radio interview with Jefferson Exchange. Most recently, I presented at the Institute for Health in the Built Environment 2019 Build Health event, where I connected with a dozen or so of my ongoing and future collaborators.
I am pleased to announce that several PLoS journals are teaming up for a special issue, titled “Microbiome Across Biological Systems”, and the call for submissions is open!
PLoS (Public Library of Science) is a non-profit publisher that fosters open-access and accessibility in science, with a variety of subject-specific journals, as well as the interdisciplinary journal, PLoS ONE. I spend a lot of my time with interdisciplinary science which doesn’t quite fit with any one field, and I appreciate journals which are interested in that intersectionality. In fact, that’s what this call is about: looking at whole microbial communities at the intersection of ecosystems, at multiple trophic levels, and where the science is interdisciplinary.
I am currently an Academic Editor at PLoS One. I’m acting as a guest editor on this open call, and I look forward to curating this exciting upcoming issue! Submit online by August 6th.
This colloquium course introduces
students to current knowledge on selected host-associated or human-associated microbiomes,
and uses that base knowledge to discuss their relevance to human health in the
context of social equity. Example topics
include the effect of diet on the microbial community in the gut and the
importance of nutrient composition of free school lunches; maternal stress and
the effect on offspring physiology, immune development, and host-microbial
interactions; microbial communities in air, air quality, and income-based
housing; building quality, indoor microbiology, and enforced occupancy (ex. prisons
or public schools); and more. Guest lectures from relevant experts will be
included as possible.
Some background in microbial
ecology, genetics, anatomy, immunology, or sociology would be helpful, but is
not required. While difficult concepts
will be discussed, the course is intended to teach students about the basic
principles and how to apply them to contemporary social issues: what is a
microbiome? How does host anatomy and health drive microbial ecology? How does environmental microbiology and building
microbiology contribute to or impinge on health? When we read about
host-associated microbiomes in the news, especially regarding health, how can
we assess if the study is rigorous and how should we interpret the scope of the
findings?
The skill-set objectives include learning to review
scientific journal articles, distilling their findings while understanding
their limitations, and developing science communication skills via written
assignments and in-class discussions.
Over the fall 2018 term, BioBE and ESBL undergrads made a project video explaining a recent publication on the effect of different daylight treatments on bacteria in dust. The post and video can be found here!
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).
BioBE and ESBL staff (not all pictured), Sept 2018
Research
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.
Teaching
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.
What better way to learn about host microbiota than an anatomically-correct dissected cat costume?
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.
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.
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.
Outreach
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.
Hannah Tavalire and I talking about ‘Gut Stuff’.
Anne Nolin and M Jackson, from ‘Ice, ice, maybe’
Science Squad.
A packed house for Krista McGuire (pictured) and Bitty Roy, ‘Featuring Fungi’
Avery McRae, a plaintiff in Julianna v. US, ‘Future Scientists’
Serena Orsinger, activist and naturalist, ‘Future Scientists’
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.
Blog
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.
Life
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.
Scientist by day, wedding officiant also by day. Well, more like scientist by day, and sometimes nights and weekends, and wedding officiant this one day. But a helluva day ❤️🧡💛💚💙💜 pic.twitter.com/qMgXy7eTJm
I am protesting having to March on a weekend, which is yet another unpaid community service that academics are expected to perform but not always given credit for. pic.twitter.com/PpjwiSZAfr
I marched (seriously and facetiously) for science.
Tired of seeing so much trash at the beach? Make your own cleanup kit and collect 4 gallons of small plastic bits from sand like we did! It's too cold to swim in the ocean anyway. pic.twitter.com/SPFTUyJwvv
Lee and I picked up trash at the beach, using a sieve he built to pick up trash.
I tried to spend more time on creative projects, including getting back into art after more-or-less tabling it for several years.
Looking Ahead
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!
The Ishaq Lab 