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:

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!

2017 Year in Review

The end of 2017 marks the second year of my website, as well as another year of life-changing events, and reflecting on the past year’s milestones help put all those long hours into perspective.  I reviewed my year last year, and found it particularly helpful in focusing my goals for the year ahead.

Looking Back

In the first half of 2017, I was working as a post-doctoral researcher in the Menalled lab at Montana State University, researching the interaction of climate change, farm management (cropping) system, and disease on soil bacteria in wheat fields, as well as the legacy effects on subsequent crops.  I am still working to analyze, interpret, and publish those results, and hope to submit several manuscripts from that project in early 2018.  In June, I began a position as a research assistant professor in the Biology and the Built Environment Center at the University of Oregon.

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This involved another large move, not only from Montana to Oregon, which has led to some awesome new adventures, but also from agriculture and animal science to indoor microbiomes and building science.   So far, it has been a wonderful learning experience for incorporating research techniques and perspectives from other fields into my work.

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2017 has been another extremely productive year for me.  I presented some work at two conferences, the Congress on Gastrointestinal Function and the Ecological Society of America meeting (additional ESA posts here and here).  While at ESA, I was able to attend the 500 Women Scientists luncheon to discuss inequality in academia as well as recommendations we could make to improve ESA and other conferences ,such as offering affordable on-site child care, and action items we could take ourselves, such as attending training workshops to combat implicit bias or making sure job searches recruit a diverse candidate pool.

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500 Women Scientist group at ESA 2017

This year, I added four new research publications and one review publication to my C.V., and received word that a massive collaborative study that I contributed to was accepted for publication- more on that once it’s available.  In April, I hosted a day of workshops on soil microbes for the Expanding Your Horizons for Girls program at MSU, and I gave a seminar at UO on host-associated microbiomes while dressed up as a dissected cat on Halloween.  In November, I participated in a Design Champs webinar; a pilot series from BioBE which provides informational discussions to small groups of building designers on aspects of how architecture and biology interact.

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I published 34 posts in 2017, including this one, which is significantly fewer than the 45 I published in 2016.  However, I have doubled my visitor traffic and views over last year’s totals: over 2,000 visitors with over 3,200 page views in 2017! My highest-traffic day was April 27th, 2017.  While I am most popular in the United States, I have had visitors from 92 countries this year!

visitor_map_webpage
Map of home countries for 2017 website visitors.

My most popular post is currently “Work-life balance: what do professors do?”, with over 610 views! My least popular is “Presentation on juniper diets and rumen bacteria from JAM 2016 available!” with just 2 views, granted, that one appeals to a much narrower audience.  This year, in addition to updates on publications, projects, and positions, I wrote about writing; including theses and grants. I wrote about getting involved in science, be it through education, participation, or legislation.  I described outreach in academia, and the process of interviewing.  I gave some perspective on the effect of climate change and anthropological influence on agriculture and ecology, as well as on the debate surrounding metrics of success in graduate study.

I also added some “life” to my work-life balance; in November, I married my best friend and “chief contributor“, Lee Warren, in a small, stress-free ceremony with some local friends in Eugene, Oregon!!

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Looking Ahead

I have high hopes for 2018, notably, I’d like to finish more of the projects that have been in development over the last two years during my post-docs.  Nearly all academics carry forward old projects: some need additional time for experimentation or writing, some get shelved temporarily due to funding or time constraints, some datasets get forgotten and gather dust, and some which got cut short because of the need to move to a new job.  This is a particular concern as grant funding and length of job postings become shorter, forcing researchers to cut multi-year projects short or finish them on their own time.  After defending in early 2015, I had two one-year postings and started at UO in June 2017, making this my fourth job in three years.  I’m looking forward to roosting for a bit, not only to clear out unfinished business, but also to settle into my new job at BioBE.  This fall, I have been analyzing data on a weatherization project, writing a handful of grants, and developing pilot projects with collaborators.  I have really enjoyed my first six months at BioBE, and Lee and I have taken a shine to Eugene.  In the next few months, I hope to have more posts about my work there, exciting new developments in BioBE and ESBL, and more insights into the work life of an academic.  Happy New Year!

Islands, Evolution, and a book report

Academics love to keep books, such that they accumulate over the years until, one day, you move offices, change universities, or retire and give them all away.  I happened upon one of these give-away treasure troves recently and grabbed several older books.  I began my journey with a historical perspective on island biogeography, and I enjoyed it so much I thought I’d write about it.

IMG_20170726_153211

The book is “The Song of the Dodo: Island Biogeography in an Age of Extinctions”, written in 1996 by David Quammen.  David is a science writer, but has also written some fiction, and at the time this book was published lived in Montana, from where I so recently emigrated.  It’s written in a meandering way, weaving together textbook information, historical accounts of ecologists from the last few centuries, and his own experiences traveling the world to visit the unique locations that inspire(d) scientists to brilliance.  While it certainly helps to have a background in biology or ecology in order to fully appreciate the book, it’s seems interesting enough to grab a more general audience.

Be prepared for a feast of delicious jargon, though:

“The Origin of Species is a book of encyclopedic richness and inexhaustible tediousness, a great potpourri of argument and fact in which a reader can find almost anything a reader might want: Lamarckism, animal husbandry, geology, ethology, experimental botany, the kitchen sink, island biogeography.” pg. 200

So what is island biogeography? It’s the study of how species are distributed across an environment; specifically on islands.  Sounds simple enough.  Let’s go back to the Age of Exploration (late 1400s to the late 1700s) when new technology and a growing appreciation for the size of the planet gave rise to a burst of exploration.  Suddenly- and this historical perspective is very Euro-centric- new lands, geology, peoples, plants, and animals were being discovered, and tales of the exotic made it back to Europe.  Sometimes, preserved animal specimens would make it back to Europe, which was extremely tricky as they had to be prepared in the field, usually by skinning or pickling.  Often, the heads, feet, tails, or wings would be removed during the process, accidentally or intentionally.  This only fueled the mystery more: many species of Birds of Paradise had their feed removed during processing, leading British ecologists, many of whom were working off secondary information and had never traveled to these locales, to believe that these birds had no feet at all and lived entirely among the clouds until their death when they fell to the ground.

birds-of-paradise_final.jpg
Birds of Paradise, Natural History Museum of Utah

The lure of discovering new, fabulous species was irresistible, and naturalists began expeditions all over the globe to make observations and collect specimens.  Largely, collectors interested in one particular animal or insect would select a small number of specimens for each species they collected, thus they accidentally missed the natural variations in size or color that one sees in wild animals.  After all, one doesn’t always notice little differences when only looking at a few examples.  Or, they would fail to record the particular location of their find, often only labeling it only by the continent on which is was collected.  But some naturalists were more curious.  They collected more specimens, more data, and began to notice patterns.

The most important pattern was that not all animals were found everywhere.  Certainly, it was noted that certain animals were specific to a habitat- sharks to the ocean, camels to the desert, etc.  But it wasn’t until people discovered animals found exclusively on islands that it really sunk in.  And this is extremely important, because it begged the question: why?  Why are some animals in one place and not another?  How did they get there?  The prevailing theories until that point were largely based on stories from the Christian bible, but with the discovery of so many new species, a literal ark was increasingly going to be improbably overcrowded.

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Geography and Evolution

Long story short, many ecologists actually began as geologists- Charles Darwin included, and in studying island formation it became understood that some island animals had crossed on land bridges, while others flew, swam, or drifted onto islands.  The species and mode of arrival very much determined whether you could then get back off the island, or whether you were stuck.  Ok, so now we know that animals can travel and change their own habitat location (which is different from migration), which went against the prevailing theory that animals were located where they had been put during a creation event.

FinchTree
Finches

The next important pattern was that multiple, closely-related species could exist in a place at the same time.  In the years following his voyage while studying the specimens he collected, Charles Darwin noticed this of the mockingbirds, tortoises, and eventually the finches on the Galapagos, which was just a brief stop on his 5 year geology cruise aboard the Beagle (1831-1836).  Again, this was important, because what was the likelihood that all these similar bird species came to the same island chain at the same time?  It was more likely that a few birds of a single species had come over, and these birds had changed over thousands of generations into several new species.  The accepted notion was that animals didn’t change- they remained as they had been created.  The idea that a species could change or evolve over time was, at best, silly and at worst, blasphemous.

Nevertheless, a number of ecologists had made reference to the possibility of change during the Age of Exploration, but lacked solid data and a concrete theory of how. The mockingbirds represented true archipelago speciation; one species came to the Galapagos islands and populations became isolated on separate islands until through genetic drift they became different species, but there were only four mockingbird types and that was little enough to go on.  On the other hand, Darwin had 31 individuals representing what he thought was 14 unrelated bird species, but it wasn’t until after his voyage, when an ornithologist properly classified the birds as all being closely-related finches, that Darwin paid any attention to them at all.  In fact, Darwin nearly missed the idea of evolution because he failed to label which island his finches came from and very little about their ecology or behavior- he had to gather missing data from other accounts for years before he could see a real pattern. To be fair, the finches are a much more complicated pattern because they display adaptive radiation; one species arrived on the islands, but populations were only transiently isolated and when they crossed paths again they were still similar enough to compete, so different species evolved to fill different ecological roles (niches) in order to avoid starvation due to competition.

Darwin’s first account of his Beagle voyage made just a brief mention of this observation on closely-related species, but it changed the life of Alfred Wallace.  Wallace came from a poor background, and eventually paid for his love of naturalism and data collection by selling the specimens he collected.  Many British naturalists at the time were wealthy, and selling one’s collection seemed base- thus Wallace, with no title or reputation, was dismissed for most of his early career.  Years after Darwin went to the Galapagos, Wallace went to South America and Indonesia and came to the same conclusion about multiple closely related species: that one species had become many.  Wallace made the jump to speciation much faster, and sent Darwin a manuscript that was frighteningly similar to the yet-unpublished Origin of Species, which Darwin had worked on for 20 years to gain enough proof to avoid being laughed at.  Social politics aside, which are discussed in the book, a joint manuscript was presented, On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection, and a year later Darwin published On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, which, incidentally doesn’t even mention Galapagos finches.

The idea of macroorganismal evolution was difficult to come by, largely because it’s a much longer process than a human can witness, and because a possible mechanism for change was completely unknown (genetics was a long way away).  By studying islands, ecologists could study evolution in miniature worlds where the pressure to stay alive was great- indeed, many species were marooned on the islands they colonized.  Studying this, and the livestock breeding industry, gave rise to the idea in Darwin’s mind of Natural Selection– that external forces could change a species over time by forcing the species to change.

Because animals are isolated on islands, they change to fit that particular ecosystem in a very visible way.  Wallace noticed this happening in his travels in South America where large rivers converged: animals that could not cross the river became isolated and there would be similar but distinct species on each side of the river.  Again, the whimsical biogeography of a deity became less probable than natural forces (food, geography, predation, competition) driving the distribution of animals and plants.  Still, it took decades to iron out the particulars of evolution, and even today people refuse to acknowledge it.

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Natural Selection, Understanding Evolution

But this book isn’t solely a historical account- all of that is setting the stage for a larger picture: extinction.  For even as island pressures select for the creation of species distinct from those found on mainlands, it also selects them for extinction.  Islands are partially or completely isolated, and this means any breeding population is small to begin with, and eventually can become inbred.  Island populations often collapse: the gene pool becomes too stagnant, a natural disaster hits, food becomes scarce, a predator appears.  Because there are only so many individuals, and because they are adapted to a very specific location, island species can’t deal with change.  Unfortunately, humans bring nothing but change.  As we develop natural land for our own use we fragment habitat, and for animals that can’t cross a city to get to the other populations, their gene pool and food options are limited.  They become reliant on very specific living conditions in their small habitat fragments, and they are more susceptible to disease, inbreeding, predators, and climate change.  The smaller the habitat, the fewer the individuals, and the ore they struggle to survive.  As humans colonize all parts of the globe we are leaving man-made islands in our wake, with marooned populations of plants and animals that find it increasingly difficult to sustain themselves- we are the cause of the mass extinction of animals and plants around the globe that only trickles into our mainstream news.

“We still argue about when it [the dodo] actually became extinct, but it probably disappeared around the 1660s.  It’s become the sort of legendary bird of extinction.  And a very important bird.  There were extinctions before and there’s been lots of extinctions since, but it was an important extinction because that was the first time, the first time in the whole of man’s history, that he actually realized he had caused the disappearance of a species.”

-interviewing Carl Jones about the extinction of the dodo, pg. 277

The level of detail provided in The Song of the Dodo is fascinating, especially because historical accounts so often lose sight of a who a person was and the journey they had to take.  Darwin wasn’t always correct, other scientists had the right theories but the wrong data to prove them, and the elitism of early science often led to the adoption of incorrect theories from otherwise brilliant men.  The book gives an honest perspective- that all scientists are trying their best to make sense of the information they have, and that it can take an extremely long time to put the entire puzzle together.  And it gives cause for hope.  While we may not be able to bring back populations of species we have pushed to the brink, life is pluripotent.  If we give the natural world some space- it’ll grow back.

My review on Plant-Microbial Interactions in Agriculture got published!

A few months ago, I was invited to submit an article to the special issue “Plant Probiotic Bacteria: solutions to feed the World” in AIMS Microbiology on the interactions between agricultural plants and microorganisms.  As my relevant projects are still being processed, I chose to write a review of the current literature regarding these interactions, and how they may be altered by different farming practices.  The review is available as open-access here!

“Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity”

A thorough understanding of the services provided by microorganisms to the agricultural ecosystem is integral to understanding how management systems can improve or deteriorate soil health and production over the long term. Yet it is hampered by the difficulty in measuring the intersection of plant, microbe, and environment, in no small part because of the situational specificity to some plant-microbial interactions, related to soil moisture, nutrient content, climate, and local diversity. Despite this, perspective on soil microbiota in agricultural settings can inform management practices to improve the sustainability of agricultural production.

Keywords bacteria; climate change; farming system; fungi; nutrient exchange; pathogens; phytohormones

Citation: Suzanne L. Ishaq. Plant-microbial interactions in agriculture and the use of farming systems to improve diversity and productivity. AIMS Microbiology, 2017, 3(2): 335-353. doi: 10.3934/microbiol.2017.2.335