OMSI presentation: A crash course on the microbiome of the digestive tract

Last night, I gave my first “science stand-up” as part of the Oregon Museum of Science and Industry (OMSI) Science Pub series at Whirled Pies in Eugene, OR.  I really enjoy giving public presentations of my work, and while I’ve been on stage with a microphone before, it was the first time I got a stool to put my drink on.

I gave a talk which encompassed much of my previous work on host-associated microbiomes in moose and other ruminants, as well as more current research from others on the human gut.  It’s difficult enough to fit the field of host-associated microbiomes into a semester-long class, nevermind an hour (I digress), so I kept it to the highlights: “A crash course on the microbiome of the digestive tract“.   You can find the slides here: Ishaq OMSI SciPub 20180208, although there is no video presentation at this time. I was honored to have such a well-attended lecture (about 120 people!) with an engaged audience, who had some really on-track questions about the intersection of microbial diversity and health.

Photo Credit: Al Lebovitz

As I’ve discussed here before, academic outreach is a sometimes overlooked, yet nevertheless extremely important, aspect of science.  The members of the general public are a large portion of our stakeholder audience, and outreach helps disseminate that research knowledge, facilitate transparency of the research process, and engage people who might benefit from or be interested in our work.  As I told the audience last night, scientists do like when people ask us about our work, but “we’re more scared of you than you are of us”.  I encourage everyone to add science to their life by getting informed, getting involved, and getting out to vote.

Thanks again to OMSI for inviting me to participate, and to Whirled Pies for hosting!


Featured Photo Credit: Al Lebovitz

What I do for a living Part 5: The Indoor Microbiome

Last June, I started a position as a Research Assistant Professor of Microbial Ecology at the Biology and the Built Environment Center at the University of Oregon.  The BioBE Center is a collaborative, interdisciplinary research team investigating the built environment – the ecosystem that humans have created for themselves in buildings, vehicles, roadways, cities, etc.  With my background in host-associated microbiology, I am concerned with how the built environment interacts with biology.


Humans shed microorganisms constantly – every itch, every cough, every minute.  In fact, our buildings are littered with the biological material shed from our bodies and our microbiomes (1, 2, 3, 4).  Pets (1, 2) and plants (1, 2) also contribute, and so does outdoor air (1, 2).  In fact, the indoor environment is full of microorganisms.


In addition to knowing how our presence, our behaviors (ex. cleaning), and how we run our buildings (ex. ventilation) creates the indoor microbiome, I want to know how the indoor microbiome affects us back.  Not only can “sick buildings” negatively affect air quality, but they can harbor more microorganisms, especially fungi, or pathogenic species which are detrimental to our health.

My first indoor microbiome data is one that I have inherited from an ongoing project on weatherization in homes, and hope to present some of that work at conferences this summer.  Since June, a large amount of my time has gone into project development and grant writing, most of which is still pending, so stay tuned for details.  It has involved read lots of articles, going to seminars, networking, and brainstorming with some brilliant researchers.

As research faculty, I am not required to teach, although I have the option to propose and teach courses by adjusting my percent effort (I would use the teaching salary to “buy back” some research salary).  As I am not currently tenure-track, I am also limited in my ability to hire and formally mentor students.  However, I have been teaching bioinformatics to a student who recently graduated with his bachelor’s and is pursuing a masters in bioinformatics later this year.

I’ve also been keeping up with my science outreach.  I gave a presentation on my host-associated microbiome work, I marched, I volunteered for a few hours at Meet A Scientist day at the Eugene Science Center, and I’m hosting a Science Pub on “A crash course in the microbiome of the digestive tract” at Whirled Pies in Eugene this Thursday, February 8th!



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.

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!

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!

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.

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.

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.

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.

Make your voice heard.