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!

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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!

Field notes from my first ESA meeting

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From iDigBio
A couple of weeks ago, I attended my first Ecological Society of America meeting in Portland, which assembles a diverse community of researchers looking at system-wide processes.  It was an excellent learning experience for me, as scientific fields each have a particular set of tools to look at different problems and our collective perspectives can solve research problems in more creative ways.

In particular, it was intriguing to attend talks on the ecology of the human microbiome.  Due to the complexity of host-associated microbial communities, and the limitations of technology, the majority of studies to date have been somewhat observational.  We have mapped what is present in different animals, in different areas of the body, under different diet conditions, in different parts of the world, and in comparison between healthy and disease states.  But given the complexity of the day-to-day life of people, and ethics or technical difficulty of doing experimental studies in humans, many of the broader ecological questions have yet to be answered.

For example, how quickly do microbial communities assemble in humans?  When you disturb them or change something (like adding a medication or removing a food from your diet) how quickly does this manifest in the community structure and do those changes last? How does dysbiosis or dysfunction in the body specifically contribute to changes in the microbial community, or do seemingly harmless events trigger a change in the microbial community which then causes disease in humans? Some of the presentations I attended have begun teasing out these problems with a combination of observational in situ biological studies, in vitro laboratory studies, and in silico mathematical modeling.  The abstracts from all the meeting presentations can be found on the meeting website under Program.  I have also summarized several of the talks I went to on Give Me The Short Version.

One of my favorite parts was attending an open lunch with 500 Women Scientists, a recently-formed organization which promotes diversity and equality in science, and supports local activists to help change policy and preconceived notions about diversity in STEM.  The lunch meeting introduced the organization to the conference participants in attendance, asked us to voice our concerns or difficulties we had faced, encouraged us to reach out to others in our work network to seek advice and provide mentoring, and walked us through exercises designed to educate on how to build a more inclusive society.

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500 Women Scientists at ESA, August 2017

My poster presentation was on Wednesday, halfway through the meeting week, which gave me plenty of time to prepare.  You never know who might show up at your poster and what questions they’ll have.  In the past, I’ve always had a steady stream of people to chat with at my poster which has led to a number of scientific friendships and networking, and this year was no different.  The rather large (but detailed) poster file can be found here: Ishaq et al ESA 2017 poster .  Keep in mind that this is preliminary work, and many statistical tests have not yet been applied or verified.  I’ve been working to complete the analysis on the large study, which also encompasses a great deal of environmental data.  We hope to have manuscript drafted by this fall on this part of the project, and several more over the next year from the research team as this is part of a larger study; stay tuned!

Presentation on maternal influences on the calf digestive tract from JAM 2016 available!

The video presentation of my work on the effects of maternal biotic influences on the developing calf digestive tract bacteria is finally available for public use!

Abstract 1522: Influence of colostrum on the microbiological diversity of the developing bovine intestinal tract

Suzanne L Ishaq, Elena Bichi, Sarah K Olivo, James Lowe, Carl J Yeoman, Brian M Alridge

 

A collaborative project on sheep feed efficiency and gut bacteria was published!

I’m pleased to announce that a paper that I contributed to was recently accepted for publication in the Journal of Animal Science!

“Feed efficiency phenotypes in lambs involve changes in ruminal, colonic, and small intestine-located microbiota”, Katheryn Perea; Katharine Perz; Sarah Olivo; Andrew Williams; Medora Lachman; Suzanne Ishaq; Jennifer Thomson; Carl Yeoman (article here).

Katheryn is an undergraduate at New Mexico Institute of Mining and Technology who received an INBRE grant to support her as a visiting researcher at Montana State University in Bozeman, MT over summer 2016.  Here, she worked with Drs. Carl Yeoman and Jennifer Thomson to perform the diversity analysis on the bacteria in the gastrointestinal tract of sheep from a previous study.  These sheep had been designated as efficient or inefficient, based on how much feed was needed for them to grow.  Efficient sheep were able to grow more with less feed, and it was thought this might be due to hosting different symbiotic bacteria which were better at fermenting fibrous plant material into usable byproducts for the sheep.

Samples from the sheep were collected as part of a larger study on feed efficiency performed by MSU graduate students Kate Perz and Medora Lachman, as well as technicians Sarah Olivo and Andrew Williams, and Katheryn performed the data and statistical analysis using some of my guidelines.  This is Katheryn’s first published article, and one I just presented a poster on at the Congress on Gastrointestinal Function in Chicago, IL!

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2017 Congress on Gastrointestinal Function

I just got back from my very first Congress on Gastrointestinal Function, poster tube.jpga small meeting for  researchers with a specific focus on the gastrointestinal tract, which is held every two years in Chicago, Illinois.  The special session this year was on “Early Acquisition and Development of the Gut Microbiota: A Comparative Analysis”.  The rest of the sessions opened up the broader topics of gut ecosystem surveillance and modulation, as well as new techniques and products with which to study the effect of microorganisms on hosts and vice versa.  The research had a strong livestock animal focus, as well as a human health focus, but we also heard about a few studies using wild animals.

As I’ve previously discussed, conferences are a great way to interact with other scientists.  Not only can you learn from similar work, but you can often gain insights into new ways to solve research problems inherent to your system by looking at what people in different fields are trying, something that you might otherwise miss just by combing relevant literature online.  A meeting or workshop is also a great place to meet other similarly focused scientists to set up collaborators that span academia, government, non-profit, and industry sectors.

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It was great to catch up with Dr. Ben Wenner, now at Purdue Agribusiness, and meet Yairy Roman-Garcia, grad student at the Ohio State University.

This year, I was excited for one of my abstracts to be accepted as a poster presentation, and honored to have the other upgraded from poster to talk!  Stay tuned for details about both of those projects in the coming weeks, and be sure to check this meeting out in April, 2019.

Plowing Forward: Montana Agriculture in a Changing Climate

Agriculture is consistently Montana’s largest economic sector, but as an arid state we need to prepare for the challenges brought on by changing weather patterns.  Yesterday, agricultural producers, scientists, special interest groups, lawmakers, and the general public came together at the Bozeman Public Library to talk about the future of climate change and what it means for people in the agricultural industry and research sector.  The event was organized by Plowing Forward, a collaborative group to coordinate local Ag. education efforts.

“If you’ve eaten today, then you’re involved in agriculture.”  -Chris Christiaens at the Plowing Forward meeting in Bozeman, MT, Feb 10, 2017

Opening remarks were led by Chris Christiaens, lobbyist and Project Specialist for the Montana Farmers Union, based in Great Falls, MT. Chris gave us some perspective on how Montana farming and ranching has changed over time, especially over the last 10 years,including changes to the growing season, harvest times, water usage, the types of plants which are able to survive here.  He reminded us that the effect of climate on agriculture affects all of us.

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Chris Christiaens, Project Specialist for Montana Farmers Union.

Next, we heard from Montana’s Senator Jon Tester, who runs a farm in northern Montana that has been in his family since 1912.  The Senator spoke to his personal experiences with farming and how his management practices had adapted over the years to deal with changing temperature and water conditions.  Importantly, he spoke about how agriculture is a central industry to the United States in ways that will become even more apparent in the coming years as the negative effects of climate change affect more and more areas.  Food security, a peaceful way of life, and economic vitality (not just in Montana or the United States, but globally), were contingent upon supporting agricultural production under adverse events.  He assured agricultural stakeholders that he continues to support production, research, and education, including the work we do in the laboratory as well as out in the field to promote agriculture.

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Montana Senator Jon Tester

Next, we heard from three professors from Montana State University.  Dr. Cathy Whitlock, a Professor of Earth Sciences, who is also the Director for the MSU Institute on Ecosystems, and a Lead Coordinator for the Montana Climate Assessment.  The Montana Climate Assessment seeks to assemble past and current research on Montana climate in order to assess trends, make predictions about the future, and help both researchers and producers to tailor their efforts based on what is happening at the regional level.  The Assessment is scheduled for release in August, 2017, and will allow for faster dissemination of research information online.

Dr. Whitlock’s introduction to the MCA was continued by  Dr. Bruce Maxwell, a Professor of Agroecology, as well as the Agriculture Sector Lead for the Montana Climate Assessment.  He summarized current research on the present water availability in Montana, as well as what we might see in the future.  He warned that drier summers were likely, and while winters may get wetter, if they continue to get warmer that snow runoff will flow into rivers before the ground has thawed.  This means snow melt will flow out of the region more quickly and not be added to local ground water sources for use here.  To paraphrase Bruce, a longer growing season does you no good if you don’t have any water.

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Dr. Bruce Maxwell, Montana State University

We also heard from my current post-doctoral advisor, Dr. Fabian Menalled, Professor of Weed Ecology Management and Cropland Weed Specialist (Extension).  He presented some of the results from our ongoing project at Fort Ellis on the interactions between climate change (hot and dry conditions), farm management system (conventional or organic), disease status, and weed competition on wheat production.  Increased temperatures and decreased moisture reduced wheat production but increased the amount of cheatgrass (downy brome), a weed which competes with wheat and can reduce wheat growth.  My work on the soil bacterial diversity under these conditions didn’t make it into the final presentation, though.  I have only just begun the data analysis, which will take me several months due to the complexity of our treatments, but here is a teaser: we know very little about soil bacteria, and the effects we are seeing are not exactly what we predicted!

Here is the video of Dr. Menalled’s presentation (just under 9 minutes):

Lastly, we heard from a local producer who spoke to his experience with ranching on a farm that had been run continuously for well over 100 years.  His talk reflected the prevailing sentiment of the presentations: that farm practices had changed over the last few decades and people in agriculture were already responding to climate change, even if previously they wouldn’t put a name to it.  The presentations concluded with a question and answer session with the entire panel, as well as a reminder that we all have the right and the obligation to be invested in our food system.  Whether we grow produce or raise livestock for ourselves or others, whether we research these biological interactions, whether we set the policy that affects an entire industry, or whether we are just a consumer, we owe it to ourselves to get involved and make sure our voice is heard.  To that end, I wrote a letter to my legislators (pictured below), and in the next few weeks I’ll be writing posts about how I participate in science (and agriculture) on the local and national level.

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Make your voice heard.

2016 Year In Review

Looking back

2016 started with a bang when I launched this site and joined Twitter for the first time!  For the first quarter of the year, I was a post-doctoral researcher in the Yeoman Lab in the Department of Animal and Range Sciences at Montana State University.  I was working on a total of eight grants, ranging from small fellowships to million dollar projects, both as a principal investigator and as a co-PI.  I was also doing the bioinformatic analysis for multiple projects, totaling nearly 1,000 samples, as well as consulting with several graduate students about their own bioinformatic analyses.

In late spring, my position in the Yeoman lab concluded, and I began a post-doctoral position in the Menalled Lab in the Department of Land Resources and Environmental Sciences at MSU.  This position gave me the opportunity to dramatically increase my skill-set and learn about plant-microbe interactions in agricultural fields.  My main project over the summer was studying the effect of climate and other stresses on wheat production and soil microbial diversity, and this fall I have been investigating the legacy effects of these stressors on new plant growth and microbial communities.  I have extracted the DNA from all of my Fort Ellis summer trial soil samples, and look forward to having new microbial data to work with in the new year.  Based on the preliminary data, we are going to see some cool treatment effects!

Over the summer, I attended the American Society for Microbiology in Boston, MA in June, where I presented a poster on the microbial diversity in organic and conventional farm soil, and the Joint Annual Meeting for three different animal science professional societies in Salt Lake City, UT in July, where I gave my first two oral conference presentations. One was on the effect of a juniper-based diet on rumen bacteria in lambs, and the other was on the biogeography of the calf digestive system and how location-specific bacteria correlate to immune-factor expression.

Thanks to a lot of hard work from myself and many collaborators, a number of research projects were accepted for publication in scientific journals, including the microbial diversity of agricultural soils, in reindeer on a lichen diet, and in relation to high-fat diets in mice, it also included work on virulent strains of Streptococcus pyogenes, and a review chapter on the role of methanogens in human gastrointestinal disease.

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Looking forward

A whopping thirteen manuscripts are still in review at scientific journals or are in preparation waiting to be submitted! Some of those are primarily my projects, and for others I added my skills to the work of other researchers.  Editing all those is going to keep me plenty busy for the next few months. I’ll also be writing several more grants in early 2017, and writing a blog post about the Herculean task that can be.

I’ll be concluding my greenhouse study by March of 2017, just in time to prepare for another field season at Fort Ellis, on the aforementioned climate change study that is my main focus. In January, I’ll be spending time in the lab helping to process and sequence DNA from my 270 soil samples, and begin the long task of data quality assurance, processing, and analysis.  I’m not worried, though, 270 samples isn’t the most I’ve worked with and bioinformatic analysis is my favorite part of the project!

This year, I am hoping to attend two conferences that I have never previously attended, and present data at both of them.  The first will be the 2017 Congress on Gut Function in Chicago, IL in April, and the second will be the Ecological Society of America’s Annual Meeting in Portland, OR in August.  Both conferences will give me the opportunity to showcase my work, network with researchers, and catch up with old friends.

If 2017 is anything like the past few years, it’s going to be full of new projects, new collaborators, new skills, and new opportunities for me, and I can’t wait!  So much of what I’ve accomplished over the last year has been possible because of the hard work, enthusiasm, and creativity of my colleagues, students, friends, and family, and I continue to be grateful for their support.  I’d also like to thank anyone who has been kind enough to read my posts throughout the last year; it’s been a pleasure putting my experiences into words for you and I appreciate the time and interest you put in.  I look forward to sharing more science with you next year!

ASM Microbe 2016 was a blast!

For the last four days I was in Boston for the American Society for Microbiology (ASM) Microbe 2016 meeting.  The meeting is held in Boston on even years, and New Orleans on odd. 
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The conference brings together all sorts of microbiologists: from earth sciences, to host-associated, to clinical pathologists and epidemiologists, to educators.  This year, there were reportedly over 11,000 participants! Because of the wide variety of topics, there is always an interesting lecture going on related to your topic, and it was a wonderful experience to be able to talk directly to other researchers to learn about the clever techniques they are using.  I posted about a tiny fraction of those interesting projects on Give Me The Short Version.

On Sunday, I presented a poster on “Farming Systems Modify The Impact Of Inoculum On Soil Microbial Diversity.”  I analyzed the data from this project for the Menalled Lab last year, and it has developed into a manuscript in review, as well as several additional projects in development.

Ishaq et al ASM 2016 poster

One of the best parts of ASM meetings is that you never know who you are going to run into, and I was able to meet up with several friends and colleagues, including Dr. Benoit St-Pierre, who was a post-doc in the Wright lab at the University of Vermont while I was a student, and Laura Cersosimo, the other Ph.D. candidate from the UVM Wright lab who will be defending in just a few months!  I also ran into Ph.D. candidate Robert Mugabi, who is hoping to defend by March and in the Barlow lab at UVM while I was there.  Most unexpectedly, I ran into a A Lost Microbiologist who had wandered in from Norway: Dr. Nicole Podnecky, who I met at UVM back when we were undergraduates!

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Of course, no conference would be complete without vendor swag.

Conference Proceedings

Scientific conferences are a great place to get your name out there, discuss research with colleagues, and meet other researchers with whom you might one day collaborate.  It can be difficult to get noticed as a graduate student or post-doctoral researcher, especially if it’s your first time at a certain conference, if your poster time conflicts with more interesting events, or if you find yourself way at the back of a 1,000 poster hall.  You need to be ready to introduce yourself and get your point across, and to do it in a memorable and concise way.  There may be hundreds or even thousands of people in attendance, so you need to make a fast impression.

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Too much info on your card? A black background is slimming.

Though a bit outdated these days, I find business cards really handy.  Not only can you quickly hand out all your information, but you can write notes on the back about what you discussed with someone so you can follow up with them later.  It’s easy to leave a bag of them at your poster for people to take, too.

Not only is your poster or presentation’s content important, its visual appeal will help draw in people who are “browsing”.  Make sure your font is large enough to read from 5-8 ft away, and that you have some color, but not enough to make text illegible.  Bolding or bulleting take-home messages can also be really helpful.  Make sure you can describe your poster in a variety of ways: in under 60 seconds to the person with a mild passing interest, and in-depth with the person that is curious about your methods or your other projects.

The most important thing to prepare, though, is yourself.  You are representing yourself, your institution, and your science.  Cleanliness, organization, and confidence make a huge difference when meeting new people, and will make you more approachable.  Make eye contact, try to avoid filler words, and smile!  I have watched posters get overwhelmingly passed by because the presenter was on their phone, or looked bored or annoyed.  Making eye contact and saying hello to someone as they walk by is often enough to get them to slow down and ask you about your work.

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If nothing else, a brightly colored shirt will attract attention to you and your poster.

When asking questions at other presentations, be sure to be polite; being demanding or rude is guaranteed to be met with disapproval from the rest of the audience.  And go ahead and introduce yourself to other researchers, just be sure to keep it brief and don’t interrupt another meeting.

One more thing to consider at a conference is your behavior outside of your presentation.  You are at a gathering of intellectuals who may one day be your boss, your colleague, your grant reviewer, or otherwise influential in your career.  They may remember that they saw you talking loudly to a friend during a presentation, or that you got too drunk at the opening session.  Conferences are often used as an excuse to take a concurrent vacation, especially for those in academia who generally can’t take a week off during the semester.  But you should remember why you are there and act professionally, especially as a graduate student or post-doc, because you never know who’ll remember you in the future.

Abstract Accepted!

Great news!  I’ll be presenting a poster this year at the American Society for Microbiology’s (ASM) Microbe Conference in Boston, MA this June 16th-20th.  I’ll have a date and time later this month, and will of course post the full abstract and poster after the presentation.

“Farming Systems Modify The Impact Of Inoculum On Soil Microbial Diversity”

Suzanne L. Ishaq¹, Stephen P. Johnson², Zach J. Miller³, Erik A. Lehnhoff4, Carl J. Yeoman¹, Fabian D. Menalled²

1 Montana State University, Department of Animal and Range Science, Bozeman, MT 2 Montana State University, Department of Land Resources & Environmental Sciences, Bozeman, MT 3 Montana State University, Western Agriculture Research Center, Bozeman, MT 4 New Mexico State University, Department of Entomology, Plant Pathology and Weed Science, Las Cruces, NM