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.
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.
Great news: you can participate in science without going through a decade of higher education (sorry grad students, but thanks for your service!). There are two ways to do this: either you can volunteer to collect samples for a project, or you can volunteer to be the sample for a project. You can volunteer through the National Institutes of Health, third-party match sites that help recruit volunteers for large projects, independent research centers (that are usually under contract to run a study), and most universities and colleges have volunteer-recruiting websites.
Get out there and collect
There is a myriad of environmental science studies that rely on volunteers to collect samples, which may take place in very specific areas, or globally. Some are simple wildlife surveys, often through conservation societies like the Audubon Society, which use volunteers’ bird sightings to estimate populations. Humanitarian volunteer agencies may recruit volunteers for global research studies, as well. Some projects require more technical sampling, or require participants to travel to distant or difficult to reach places, and thus rely on outdoors-people with the gear and ability to safely retrieve water, soil, plants, animal hair or feces, you name it! There are some excellent examples of global projects which can be found through Adventure Scientists. AS recruits and trains volunteers for more difficult environmental sampling, and I am currently participating in their Gallatin Microplastics Initiative (year 1 and 2) along with my sampling team: Lee and Izzy.
‘Host’ your own research
Volunteering to be the sample also allows you to participate on a sliding scale of involvement. For example, observational studies only collect information on what is already happening. These might be sociology (human behavior) studies which only require you to fill out surveys (often online) on your personal history or normal routines. You can also donate biological samples (hair, breathe, blood, urine, feces, skin scrapings, etc.) which are minimally invasive but don’t necessarily require any experimental treatments that you have to participate in. A study that I analyzed data for asked participants to use a breathalyzer and submit a fecal sample in a jar. That’s all, and they were financially compensated for their time. The study was trying to correlate microorganisms in the gut with how much hydrogen or methane was in the breath, and whether a breathalyzer test could be used as a rough measure of how many methanogenic archaea lived in your gut. Often, research centers which are focused on medical treatment for a specific disease will collect specific biological samples.
Studies which require actual treatments or testing are clinical medical studies that rely on human volunteers upon whom to test products. At a certain point in drug or vaccine testing, animal or computer models can no longer serve as a proxy and you need to test things in humans. Thanks to HIPPA (Health Insurance Portability and Accountability Act of 1996) and other safety regulations, both at the federal and institutional level, there is a lot of transparency in these studies. You are told exactly what you will be required to do, what data will be collected and who will have access to it, and any possible health concerns that may arise from this study. Any release of tissue “ownership” will require you to sign consent.
I have participated in antibacterial product testing, a diet study investigating dairy fats during which I could only eat the prescribed diet for two solid months (boy, did I miss chocolate and Thai food!), and a study on chronic back pain (I was in the control group). For the back pain study, I had an EEG net put on my head to measure brainwaves and motion capture balls(examples below) attached all over my body to track my muscle movements as I performed simple tasks that required me to use my lower back muscles. I even had a functional MRI brain scan to measure how muscle pain might change brain function, unfortunately, I was not able to get a photocopy of my brain scan for posterity. The more invasive, time consuming, or risky a study may be, the higher the compensation (some vaccine studies compensate several thousand dollars).
You can participate in science in other ways, too. Try getting involved with science education! There are workshops, summer programs, or school events which encourage kids to learn about science and consider a career in it. Even if you aren’t a scientist yourself and can’t be a presenter, many programs still need people to chaperone, coordinate or market the event, and cater. Many science museums and educational centers have programs, as do many colleges. You can also find opportunities through local government to help clean natural sites or educate the public.
While you are out there collecting water samples from Arctic ice, counting wolves, or surveying land for public use, you are also perfectly situated to help with a little environmental restoration. The Global Microplastics Initiative looks for plastic in water sources from some very remote locations, and this study wouldn’t have been conducted if plastic in the environment wasn’t a concern. So while you are out there, try to leave the area a little cleaner than how you found it. You can volunteer for clean-up events to target specific locations that need help, but you don’t even need to organize for this one, just go out and start picking up trash!
Finally, most agricultural research studies rely on farmers, ranchers, growers, and producers as a source of project resources (like seeds, land, or cows) and project motivation. After all, federally and state-funded agricultural science exist to help local and national agriculture. You can participate in science by identifying problems that need to be solved and providing objectives for our studies, or by allowing research projects to use your land, animals, or facilities.
So far, you’ve educated yourself on science, and now you can go out and participate. Stay tuned in the next for weeks for Anyone can Science, Step 3: be supportive.
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.
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!
Several years ago, during my Ph.D. at the University of Vermont, I provided wet-lab and DNA sequence analysis work for a project investigating the health effects of a low or high fat diet on mice with Dr. Huawei Zeng of the USDA Agricultural Research Service. It was just recently published in the Journal of Nutritional Biochemistry!
Consumption of an obesigenic/high-fat diet (HFD) is associated with a high colon cancer risk and may alter the gut microbiota. To test the hypothesis that long-term high-fat (HF) feeding accelerates inflammatory process and changes gut microbiome composition, C57BL/6 mice were fed HFD (45% energy) or a low-fat (LF) diet (10% energy) for 36 weeks. At the end of the study, body weights in the HF group were 35% greater than those in the LF group. These changes were associated with dramatic increases in body fat composition, inflammatory cell infiltration, inducible nitric oxide synthase protein concentration and cell proliferation marker (Ki67) in ileum and colon. Similarly, β-catenin expression was increased in colon (but not ileum). Consistent with gut inflammation phenotype, we also found that plasma leptin, interleukin 6 and tumor necrosis factor α concentrations were also elevated in mice fed the HFD, indicative of chronic inflammation. Fecal DNA was extracted and the V1–V3 hypervariable region of the microbial 16S rRNA gene was amplified using primers suitable for 454 pyrosequencing. Compared to the LF group, the HF group had high proportions of bacteria from the family Lachnospiraceae/Streptococcaceae, which is known to be involved in the development of metabolic disorders, diabetes and colon cancer. Taken together, our data demonstrate, for the first time, that long-term HF consumption not only increases inflammatory status but also accompanies an increase of colonic β-catenin signaling and Lachnospiraceae/Streptococcaceae bacteria in the hind gut of C57BL/6 mice.
A manuscript that I helped co-author, “Rumen and cecum microbiomes in reindeer (Rangifer tarandus tarandus) are changed in response to a lichen diet and may effect enteric methane emissions” was just accepted for publication in PLOS ONE. In 2012 I went to Norway to apprentice for two weeks in the lab of Dr. Monica Sundset, and in 2013, Monica’s graduate student Alex came to the University of Vermont to apprentice in Dr. Andre Wright’s lab, where I taught him quantitative real-time PCR and some bioinformatics. Alex performed a feeding trial back in Norway, in which reindeer were fed a lichen-based diet, in order to assess changes in microbial diversity. Lichens contain usnic acid, which is toxic to ruminants. Reindeer; however, host some unique bacteria which degrade usnic acid in the rumen and allow the reindeer to eat them without dietary problems.
Reindeer (Rangifer tarandus tarandus) are large Holarctic herbivores whose heterogeneous diet has led to the development of a unique gastrointestinal microbiota, essential for the digestion of arctic flora, which may include a large proportion of lichens during winter. Lichens are rich in plant secondary metabolites, which may affect members of the gut microbial consortium, such as the methane-producing methanogenic archaea. Little is known about the effect of lichen consumption on the rumen and cecum microbiotas and how this may affect methanogenesis in reindeer. Here, we examined the effects of dietary lichens on the reindeer gut microbiota, especially methanogens. Samples from the rumen and cecum were collected from two groups of reindeer, fed either lichens (Ld: n = 4), or a standard pelleted feed (Pd: n = 3). Microbial densities (methanogens, bacteria and protozoa) were quantified using quantitative real-time PCR and methanogen and bacterial diversities were determined by 454 pyrosequencing of the 16S rRNA genes.
In general, the density of methanogens were not significantly affected (p>0.05) by the intake of lichens. Methanobrevibacter constituted the main archaeal genus (>95% of reads), with Mbr. thaueri CW as the dominant species in both groups of reindeer. Bacteria belonging to the uncharacterized Ruminococcaceae and the genus Prevotella were the dominant phylotypes in the rumen and cecum, in both diets (ranging between 16–38% total sequences). Bacteria belonging to the genus Ruminococcus (3.5% to 0.6%; p = 0.001) and uncharacterized phylotypes within the order Bacteroidales (8.4% to 1.3%; p = 0.027), were significantly decreased in the rumen of lichen-fed reindeer, but not in the cecum (p = 0.2 and p = 0.087, respectively). UniFrac-based analyses showed archaeal and bacterial libraries were significantly different between diets, in both the cecum and the rumen (vegan::Adonis: pseudo-F<0.05). Based upon previous literature, we suggest that the altered methanogen and bacterial profiles may account for expected lower methane emissions from lichen-fed reindeer.”