Accepted a tenure track faculty position at the University of Maine, Orono!

I’m thrilled to announce that this fall I’ll be starting as a tenure-track Assistant Professor in animal microbiome studies at the University of Maine, Orono, in the Department of Animal and Veterinary Sciences!!!

I’ll be returning to the field I started in; gut microbiology, but I’ll be integrating things I picked up along the way over the past few years, including ongoing collaborations in soil and built environment microbiology. I’ll be right at home in the UMaine School of Food and Agriculture, which brings together animal science, nutrition, and plant and soil science.

In addition to formally starting my own lab, I’m looking forward to snowy winters and summers on the rivers.

In fact, I’ll be right at home anywhere in Orono.

Cookies in the Featured Image are from Mug Buddy Cookies, made in Biddeford, Maine!!

Microbes and social equity preprint available!

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

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

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

Abstract

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


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

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

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

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

Invited to give a talk at the XXII UANL-Engorda de Bovinas en Corral Symposium!

I’ve been invited to give a talk at the XXII UANL-Engorda de Bovinos en Corral Symposium, in Monterrey, Mexico on October 1st! My talk, “Microbial livestock: raising cattle with good microbes in mind”, will be about improving cattle production using microbial means. The most exciting part is that this will be my first trip to Mexico!

Review on ‘health in the built environment’ available online

The review on health in the built environment, led by undergrad (now post-bac) Patrick Horve and which I acted as managing author, is available online here, and an open-access, view-only version is available here.  It’s part of the Healthy Building special issue from the Journal of Exposure Science & Environmental Epidemiology.  


Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment. Patrick F. Horve, Savanna Lloyd, Gwynne A. Mhuireach, Leslie Dietz, Mark Fretz, Georgia MacCrone, Kevin Van Den Wymelenberg & Suzanne L. Ishaq.  Journal of Exposure Science & Environmental Epidemiology (2019) 

Abstract

In the constructed habitat in which we spend up to 90% of our time, architectural design influences occupants’ behavioral patterns, interactions with objects, surfaces, rituals, the outside environment, and each other. Within this built environment, human behavior and building design contribute to the accrual and dispersal of microorganisms; it is a collection of fomites that transfer microorganisms; reservoirs that collect biomass; structures that induce human or air movement patterns; and space types that encourage proximity or isolation between humans whose personal microbial clouds disperse cells into buildings. There have been recent calls to incorporate building microbiology into occupant health and exposure research and standards, yet the built environment is largely viewed as a repository for microorganisms which are to be eliminated, instead of a habitat which is inexorably linked to the microbial influences of building inhabitants. Health sectors have re-evaluated the role of microorganisms in health, incorporating microorganisms into prevention and treatment protocols, yet no paradigm shift has occurred with respect to microbiology of the built environment, despite calls to do so. Technological and logistical constraints often preclude our ability to link health outcomes to indoor microbiology, yet sufficient study exists to inform the theory and implementation of the next era of research and intervention in the built environment. This review presents built environment characteristics in relation to human health and disease, explores some of the current experimental strategies and interventions which explore health in the built environment, and discusses an emerging model for fostering indoor microbiology rather than fearing it.

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.

Symposium presentation at 2019 Joint AFS-TWS Meeting

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”

Spring Updates

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.

PLoS “Microbiome Across Biological Systems” Call for Papers!

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.

What is a microbiome? Asking for a friend.

If you find that the word ‘microbiome’ has crept into your lexicon but you don’t really know what it means or how to use it – fear not, you’re not alone. Microbiome is a new-ish term to describe something that has been studied for almost a century: the collection of microorganisms in a dynamic ecosystem, including who they are and what they are doing.

Picture a crowd of humans. Maybe this one:

Image result for crowd oregon
Image Source: Wikimedia Commons, 2017-09-09 Oregon Ducks vs. Nebraska Cornhuskers

The picture is just one instant in an event involving hundreds or thousands of organisms that were all doing a lot of different things, sometimes for just a few seconds. How would you describe it?

Maybe using the number of members present in this community? Or a list of names of attendees? The 16S rRNA gene for prokaryotes, or the 18S rRNA or ITS genes for eukaryotes, for examples, would tell us that. Those genes are found in all types of those organisms, and is a pretty effective means of basic identification. But, it’s only as good as how often that gene is found in the organisms you are looking for. There is no one gene that’s found exactly the same in all organisms, so you might need to target multiple different identification genes to look at all the different types of microorganisms, such as bacteria, fungi, protozoa, or archaea. Viruses don’t share a common gene across types, to look at viruses you’d need something else.

From our identification genes we could identify all the organisms wearing yellow; ex. phylogenetic Family = Ducks. That wouldn’t tell us if they were always found in this ecosystem (native Eugene population) or just passing through (transient population), but we could figure that out if we looked at every home game of the season and found certain community members there time and again.

But knowing they are Ducks doesn’t tell us anything else about that community member. What will they do if it starts raining? Are they able to go mountain biking? Perhaps we could identify their potential for activity by looking at the objects they are carrying? That would be akin to metagenomics, identifying all the DNA present from all the organisms, which tells us what genes are present, but not if they are currently or ever used. It can be challenging to interpret: think of sequencing data from one organism’s genome as one 1,000,000-piece puzzle and all the genomes in a community as 1,000 1,000,000-piece puzzles all dumped in a pile. In the crowd, metagenomics would tell us who had a credit card that was specifically used to buy umbrellas, but not whether they’d actually use the umbrella if it rains (ex. Eugeneans would not).

We could describe what everyone is doing at this moment. That would be transcriptomics, identifying all the RNA to determine which genes were actively being transcribed into proteins for use in some cellular function. If we see someone in the crowd using that credit card for an umbrella (DNA), the receipt would be the RNA. RNA is a working copy you make of the DNA to take to another part of the cell and use as a blueprint to make a protein. You don’t want your entire genome moving around, or need it to make one protein, so you make a small piece of RNA that will only hang around for a short period before degrading (i.e. you crumpling that RNA receipt and throwing it away because who keeps receipts anymore).

Using transcriptomics, we’d see you were activating your money to get that umbrella, but we wouldn’t see the umbrella itself. For that, we’d need metabolomics, which uses chemistry and physics instead of genomics, in order to identify chemicals (most often proteins). Think of metabolomics as describing this crowd by all the trash and crumbs and miscellaneous items they left behind. It’s one way to know what biological processes occurred (popcorn consumption and digestion).

Image result for metabolomics
Image Source: Wikimedia Commons, Metabolomics

From a technical standpoint, researching a microbiome might mean looking at all the DNA from all the organisms present to know who they are and of what they are capable. It might also mean looking at all the RNA present, which would tell you what genes were being used by “everyone” for whatever they were doing at a particular moment. Or you might also add metabolomics to identify all the chemical metabolites, which would be all the end products of what those cells were doing, and which are more stable than RNA so they could give you data about a longer frame of time. Collectively, -omics are technology that looks at all of a certain biological substance to help you understand a dynamic community. However, it’s important to remember that each technology gives a particular view of the community and comes with its own limitations.