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!
I just got back from my very first Congress on Gastrointestinal Function, a 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.
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.
According to National Day Calendar, it’s National Employee Appreciation Day! Many organizations have an annual Staff Appreciation Day or Week, and rightly so. Research staff in academia, as well as general staff, are often quietly under appreciated. Research staff can be costly, especially because many universities insist that research positions have salary and benefits fully-funded by grants. Many labs thus rely on undergraduate student researchers, who work for minimum wage or might even pay for university “research credits”, to help provide labor.
While many undergraduates find themselves performing unglamorous routine lab maintenance (anything from washing dishes, to pre-weighing commonly used supplies, to dusting, to inventory), as a researcher I can attest to how vital these tasks are. Working in a molecular biology lab, dust and other contaminants had to be minimized and it was extremely helpful to have undergraduates who were able to dust multiple times a day. When culturing bacterial isolates, I would go through hundreds of culturing tubes every week, which all needed to be autoclave sterilized, emptied, washed, and re-sterilized. This was a massive amount of effort unto itself, and I would not have been able to accomplish my culture work without. Perhaps the best example was my study of probiotics in newborn lambs. I had 24 lambs which were only 4 days old, which needed to be fed every 4-5 hours, sometimes by hand, as well as weighed, sampled, and cleaned on a regular basis. Without numerous undergraduate volunteers, I would have found myself sleeping at the barn for two months.
Not only is it polite to appreciate the staff who keep your work moving, but proper gratitude can go a long way towards improving work relationships, job satisfaction, and performance. So get out there and start thanking!
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.
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!
Every political season brings about uncertainty regarding the future of policy, funding, and cultural beliefs, and the field of science is no exception. The surprising results this November have led many scientists and other academics to fear for their jobs and research in the coming years.
Part of this stems from a growing trend of members of the public distrusting scientists (discussed here), or the rise of false information regarding serious issues such as climate change, genetically modified organisms (GMOs), vaccinations, etc., that is leading to a disparity between what scientists accept as true and what the public accepts as true. Regardless of which side of an issue you fall on, the consensus seems to be that the public is lacking scientific literacy and scientists are lacking in public outreach (hence the basis for my website).
Some of this disparity develops from public opinion and governmental policy, which can affect what research is deemed important enough to be funded. For example, if an administration denies the existence and causes of climate change, it sends a message to the public that this research and this theory are invalid or unimportant. Not only can this influence state and federal policy (1, 2), but usually means that the field is unlikely to receive state or federal research grant funding. Not only does this prevent a better understanding of scientific issues, like climate change, but it prevents technological advances which improve quality of life and the economy, especially since a good deal of commercial technology companies utilize basic research from academic institutions as publications and raw date are typically publicly available.
“The Changing Nature of U.S. Basic research: Trends in Performance”, SSTI. U&C = universities and colleges.
It also means that people relying on research grants for salary (like myself, and most other post-doctoral researchers, research associates, graduate and undergraduate researchers, technicians, and some extension outreach personnel) find themselves without jobs. Research-based salary also means that you are limited to a short contract based on the project, anywhere from a month to several years. From experience, a short-term funded position (a year or less) means that you spend a significant amount of time applying to other jobs (a lengthy process) or writing more research grants (an incredibly lengthy process that I’ll discuss in a few months- which take at least 6 – 8 weeks just to write). This can impede on your other job or social responsibilities.
Prior to the jump in federal funding during the Cold War, research was funded by universities themselves and smaller organizations. Most large-scale research grants in the last 50 years, however, have been federally funded. Organizations such as the United States Department of Agriculture (USDA), the National Science Foundation (NSF), the National Institutes of Health (NIH), the National Aeronautics and Space Administration (NASA), the US Department of Defense (DoD), the US Department of Energy (DoE), and others release funding calls on a regular basis. Some funding calls are general and will accept any project type, but many are specific to a particular field or research question (e.g. climate change, cancer, etc.). There are many other organizations or companies which will fund research in a very specific field (such as Sustainable Agriculture Research and Education (SARE), which funds organic and sustainable agriculture), or provide small fellowships. Philanthropic organizations also fund research, usually targeted towards a specific disease or special interest, and tend to be small but which can help bring funding to obscure fields.
While the total dollar amount of money put into research and development (R & D) in the US has dramatically increased over the last 50 years, the amount the federal government has been putting in has remained relatively stable over the last 10 years. Some cite the availability of other funding sources, such as universities themselves, as making up more of the costs. However, this also comes with a price, as the reduction in state funding has been cited as the cause for rising tuition, and universities are unwilling to reduce tuition even after funding has been reinstated.
The increase in funding has largely been in biomedical and engineering fields, with other areas of research remaining relatively stable.
Laboratory equipment and technology is much more complex and expensive than it was even a decade ago. The percentage of funding going into basic research, from multiple funding sources, has also declined over the last 10 years, which means research projects have to focus on short-term goals instead of long-term, complex projects that gather more data. Basic research aims to understand a system, rather than manipulate it or develop a product, and is the necessary first step which opens up decades of further, more applied, research.
The increase in number of researchers and projects/researcher, coupled with funding stagnation, can massively increase grant competition. Over the past few years, it has been holding steady at 22% for NSF, and 18-25% for NIH, although their data is more complicated because they saw an increase in budget and an increase in total number of PIs funded, yet a reduction in percent of projects funded (indicating that more many more grants were submitted overall). The USDA is also more complicated to track because of the number of grant programs within the USDA, each of which put forward different targeted grant funding calls each year. In 2013, USDA AFRI had a 10% funding success rate. Manually checking grant funding calls reveals grant-specific success rates, upwards of 30% funding success; however, many of these grants with a higher rate of success also require you to match their funding with funding from another source. So if you have a 1/3 chance of getting that USDA grant, and a 1/5 chance of getting a matching NIH grant, your actual chances of getting all that funding are 1/3 x 1/5 = 1/15.
Taken altogether, the clearest trend regarding research in the US is that it’s an integral part to our way of life and it’s not going anywhere. Whatever your political views, it’s important that scientists, citizens, and politicians come together across the aisle to do what’s best for the future of the US, and that’s going to necessitate a strong support of scientific work.
Finals are upon us and that can only mean that I’ve committed myself to reading a stack of manuscripts that students wrote as the final project for the bioinformatics lab I am teaching! This semester we took raw 16S rRNA sequencing data, analyzed it, interpreted it, and here are the results. Many of my students had never used command line based programs at the beginning of the semester, and now they can discuss the merits of different clustering techniques- I am so proud of them!
A review chapter that I put together last year is now available online or by purchasing the textbook! The chapter explores the current breadth of knowledge about methanogenic archaea that live in the human digestive tract and their involvement in human gut diseases. These archaea produce methane using hydrogen and carbon products that bacteria create during fermentation, and it’s unclear how the interaction of host immune system, bacterial diversity, and archaeal diversity can trigger disease or convalescence.
Dr. Benfang Lei is an associate professor here at Montana State University in the Department of Microbiology and Immunology, who has previously collaborated with my previous post-doc advisor, Dr. Carl Yeoman. As a lab member at the time, I consulted with Dr. Lei about the whole-genome shotgun sequencing that his lab group had performed on several Streptococcus pyogenes isolates. S. pyogenes is pathogenic in humans and, among other symptoms, causes fever for which it is named. Some of Dr. Lei’s isolates were much more virulent than others, and his study was to identify differences in the genome that would account for this. I helped perform some of the genome processing and analysis, and am happy to be a small part of such an interesting study.
Wenchao, Feng, Dylan Minor, Mengyao Liu, Jinquan Li, Suzanne Ishaq, Carl Yeoman, and Benfang Lei. 2016. Null Mutations of Group A Streptococcus Orphan Kinase RocA: Selection in Mouse Infection and Comparison with CovS Mutations in Alteration of in vitro and in vivo Protease SpeB Expression and Virulence. Infection and Immunity.
a small meeting for researchers with a specific focus on the gastrointestinal tract, which is held every two years in Chicago, Illinois. The 
The Ishaq Lab 