Research article for young scientists published!

I tried something new last new, I helped rewrite an already published study into a version specifically for young scientists, aged 10-18. Ashkaan Fahimipour, the lead author on the original research article examining the effect of light on bacterial communities in household dust, brought up the idea while we were working together at BioBE.

The journal is called Frontier for Young Minds, and pairs a young scientist with an established scientist to review your articles, a ~1,500 word summary version. The journal provides cartoon illustrations that help bring your science to life.

Ours was written by an undergrad I was mentoring at UO, Sam Rosenberg, and architecture grad student Julia May helped us with our Figures. I wasn’t involved with the original article, but along with Ashkaan, I helped Sam draft the summary as non-technical summaries of highly-technical science can be a real challenge. Check it out!

Rosenberg, S., Ishaq, S., May, J., Fahimipour, A.K. 2020. How light exposure changes bacterial communities in household dust. Frontiers for Young Minds. Article.

DNA double helix with dollar signs as a nucleotide.

The cost of scientific publishing

I’ve published a lot this year. More than normal, since I had 5 months with extra time and the knowledge that I would not be able to devote time to old projects if I began a tenure-track position. It’s been wonderful to publish so many projects, especially ones that had been languishing. But publishing fees can be steep, and often the grant is spent out by the time you publish, leaving researchers struggling to pay to get their results out. The more prestigious the journal, typically; the higher the cost. This encourages many authors to turn to lower impact or less reputable journals, which in turn causes colleagues to be suspicious of the article and may hurt their ability to get more grant money or promotion. On top of the base article processing charge (APC), there may be additional fees to print color photos, supplemental information, or to make the article open-access (readable without a journal subscription).

I’ve published 10 articles in 2019, only a fraction of what I contributed to paying for (thank you, collaborators!!). All costs are presented as 2019 fees in USD. Some journals charge less if you are a member of their society, or have financial assistance, but I’ve included the prices we paid.


Animal: $2835 APC flat rate (includes open-access)

Basic and Applied Ecology: $2000 APC for non-members (includes open-access)

Buildings: $1006 APC (always open-access)

Geoderma: $3350 APC for open-access and $2052.30 for printing 6 figures in color.

Indoor Air: $4300 APC for open-access

Journal of Animal Science: $1300 APC ($100/page member price x 10 pages + $500 color figure charge)

Journal of Exposure Science and Environmental Epidemiology: $3760 APC (includes open-access)

PeerJ: $1095 APC (always open-access). PeerJ also gives discounts for acting as a reviewer, though not applied here.

PLoS Biology: $0 APC for essays because they are published in the magazine (always open access)

PLoS ONE: $1595 APC (always open-access)

Total cost: $21,241


Keep in mind, I’m an editor for two journals and a reviewer for over a dozen, none of which I get paid for. Initial reviews take 2-4 hours, and follow up reviews on revised manuscripts can take 1-2 hours per revision (usually no more than 2 rounds). Editorial takes 1-2 hours per manuscript total, depending on the ease of finding reviewers and the completeness of those reviews. I estimate I’ve provided $3,240 (net) in editorial and review services this year alone.

Microbes and Social Equity essay published!

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

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


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

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

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

Abstract

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

Pilot study published on chemicals and bacteria in house dust.

In October 2017, Dr. Rich Corsi came to visit Oregon for two weeks during a sabbatical from the University of Texas, Austin. During his stay, Rich and I, and other BioBE/ESBL researchers chatted about doing a pilot study that would bring UT’s indoor chemistry work together with BioBE’s indoor microbial work.

Since we began our collaboration in the fall of 2017, only one of the research team is still in their original position (Jeff Kline at ESBL)! Rich Corsi, Ying Xu, and myself have all gone on to faculty positions elsewhere, graduate student Chenyang Bi defended and started a post-doc position, and the two undergrads working with me, Susie Nunez and Samantha Velazquez, graduated and went on to other things! Science collaborations work best when they can stand the test of time and geography. The benefit to everyone moving around is that you are able to hold collaboration meetings in new and exciting places each time.


In addition to the literature review we collaborated on, we eventually did get a research pilot running, and it has now been published in PeerJ!

Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community.

Samantha Velazquez1, Chenyang Bi 2,3, Jeff Kline 1,4, Susie Nunez1, Richard Corsi 3,5, Ying Xu 3,6, Suzanne L. Ishaq1,7*

Affiliations:

1 Biology and the Built Environment Center,  University of Oregon, Eugene, OR, 97403

2 Department of Civil Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 (current)

3 Department of Civil, Architectural and Environmental Engineering, University of Texas, Austin, TX 78712

4 Energy Studies and Buildings Laboratory, University of Oregon, Eugene, OR, 97403

5 Fariborz Maseeh College of Engineering and Computer Science, Portland State University, Portland, OR 97207 (current)

6 Department of Building Science, Tsinghua University, 100084, Beijing, P. R. China (current)

7 School of Food and Agriculture, University of Maine, Orono, ME 04469 (current)

Abstract

Di-2-ethylhexyl phthalate (DEHP) is a plasticizer used in consumer products and building materials, including polyvinyl chloride flooring material. DEHP adsorbs from material and leaches into soil, water, or dust, and presents an exposure risk to building occupants by inhalation, ingestion, or absorption.  A number of bacterial isolates are demonstrated to degrade DEHP in culture, but bacteria may be susceptible to it as well, thus this study examined the relation of DEHP to bacterial communities in dust.  Polyvinyl chloride flooring was seeded with homogenized house dust and incubated for up to 14 days, and bacterial communities in dust were identified at days 1, 7, and 14 using the V3-V4 regions of the bacterial 16S rRNA gene.  DEHP concentration in dust increased over time, as expected, and bacterial richness and Shannon diversity were negatively correlated with DEHP concentration.  Some sequence variants of Bacillus, Corynebacterium jeddahense, Streptococcus, and Peptoniphilus were relatively more abundant at low concentrations of DEHP, while some Sphingomonas, Chryseobacterium, and a member of the Enterobacteriaceae family were relatively more abundant at higher concentrations.  The built environment is known to host lower microbial diversity and biomass than natural environments, and DEHP or other chemicals indoors may contribute to this paucity.


Paper published on effect of farming systems on soil bacteria!

After several years of bouncing through internal and external review, I’m pleased to announce that the first microbes paper out of the Montana State University Fort Ellis project has been published in Geoderma! The Fort Ellis research has encompassed multiple labs, projects, and many personnel, as it was a large collaboration looking at the effect of different farming systems on biodiversity at the macro (plant), mini (insect), and micro (-be) levels. Spanning multiple years, this project has been a massive undertaking that I briefly participated in but anticipate getting four publications out of (two more are in preparation).

Winter wheat

I previously presented this work at the 2017 Ecological Society of America (ESA) conference (poster: Ishaq et al ESA 2017 poster). And this field soil was the “soil probiotic” that was used in the follow-up greenhouse trial that I ran which was also published this year.


Soil bacterial communities of wheat vary across the growing season and among dryland farming systems.

Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Geoderma 358:113989.

Abstract

Despite knowledge that management practices, seasonality, and plant phenology impact soil microbiota; farming system effects on soil microbiota are not often evaluated across the growing season.  We assessed the bacterial diversity in soil around wheat roots through the spring and summer of 2016 in winter wheat (Triticum aestivium L.) in Montana, USA, from three contrasting farming systems: a chemically-managed no-tillage system, and two USDA-certified organic systems in their fourth year, one including tillage and one where sheep grazing partially offsets tillage frequency. Bacterial richness (range 605 – 1174 OTUs) and evenness (range 0.80 – 0.92) peaked in early June and dropped by late July (range 92 – 1190, 0.62-0.92, respectively), but was not different by farming systems.  Organic tilled plots contained more putative nitrogen-fixing bacterial genera than the other two systems.  Bacterial community similarities were significantly altered by sampling date, minimum and maximum temperature at sampling, bacterial abundance at date of sampling, total weed richness, and coverage of Taraxacum officinale, Lamium ampleuxicaule, and Thlaspi arvense.  This study highlights that weed diversity, season, and farming management system all influence soil microbial communities. Local environmental conditions will strongly condition any practical applications aimed at improving soil diversity, especially in semi-arid regions where abiotic stress and seasonal variability in temperature and water availability drive primary production. Thus, it is critical to incorporate or address seasonality in soil sampling for microbial diversity.

‘Microbes and Social Equity’ essay accepted for publication!

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

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

Five new publications in June! (updated)

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. AnimalAccepted.

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!

A study on the effect of diet particle size got published!

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.

Ruminants, like sheep, goats, cows, deer, moose, etc.,  have a four-chambered stomach, the largest of which is called the rumen.  The rumen houses symbiotic microorganisms which break down plant fibers that the animal can’t digest on its own.  It’s estimated that up to 80% of a ruminant’s energy need is met from the volatile fatty acids (also called short-chain fatty acids) that bacteria produce from digesting fiber, and that up to 85% of a ruminant’s protein need is met from microbial proteins.

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.


Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed.

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

  1. Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
  2. Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America
  3. 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.

Woman dressed in a costume of a dissected cat, to teach a class on Halloween.

2018 Year in Review

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.

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.

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.

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.


I marched (seriously and facetiously) for science.

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!

A collaborative paper on zinc and rumen bacteria in sheep got published!

Zinc is an important mineral in your diet; it’s required by many of your enzymes and having too much or too little can cause health problems. We know quite a bit about how important zinc is to sheep, in particular for their growth, immune system, and fertility.  We also know that organically- versus inorganically-sourced zinc differs in its bio-availability, or how easy it is for cells to access and use it.  Surprisingly, we know nothing about how different zinc formulations might affect gut microbiota, despite the knowledge that microorganisms may also need zinc.

This collaborative study was led by Dr. Whit Stewart and his then-graduate student, Chad Page, while they were at Montana State University (they are now both at the University of Wyoming).   Chad’s work focused on how different sources of zinc affected sheep growth and performance (previously presented, publication forthcoming), and I put together this  companion paper examining the effects on rumen bacteria.

The pre-print is available now for Journal of Animal Science members, and the finished proof should be available soon. JAS is the main publication for the American Society of Animal Science, and one of the flagship journals in the field.


Zinc amino acid supplementation alters yearling ram rumen bacterial communities but zinc sulfate supplementation does not.

Ishaq, S.L., Page, C.M., Yeoman, C.J., Murphy, T.W., Van Emon, M.L., Stewart, W.C. 2018. Journal of Animal Science. Accepted. Article.

Abstract

Despite the body of research into Zn for human and animal health and productivity, very little work has been done to discern whether this benefit is exerted solely on the host organism, or whether there is some effect of dietary Zn upon the gastrointestinal microbiota, particularly in ruminants. We hypothesized that 1) supplementation with Zn would alter the rumen bacterial community in yearling rams, but that 2) supplementation with either inorganically-sourced ZnSO4, or a chelated Zn amino acid complex, which was more bioavailable, would affect the rumen bacterial community differently. Sixteen purebred Targhee yearling rams were utilized in an 84 d completely-randomized design, and allocated to one of three pelleted dietary treatments: control diet without fortified Zn (~1 x NRC), a diet fortified with a Zn amino acid complex (~2 x NRC), and a diet fortified with ZnSO4 (~2 x NRC). Rumen bacterial community was assessed using Illumina MiSeq of the V4-V6 region of the 16S rRNA gene. One hundred and eleven OTUs were found with > 1% abundance across all samples. The genera PrevotellaSolobacteriumRuminococcusButyrivibrioOlsenellaAtopobium, and the candidate genus Saccharimonas were abundant in all samples. Total rumen bacterial evenness and diversity in rams were reduced by supplementation with a Zn-amino-acid complex, but not in rams supplemented with an equal concentration of ZnSO4, likely due to differences in bioavailability between organic and inorganically-sourced supplement formulations. A number of bacterial genera were altered by Zn supplementation, but only the phylum Tenericutes was significantly reduced by ZnSO4 supplementation, suggesting that either Zn supplementation formulation could be utilized without causing a high-level shift in the rumen bacterial community which could have negative consequences for digestion and animal health.

Featured Image Source: Wikimedia Commons