Sequencing Wild Cat Scat
It’s not every day that you get to hear students excitedly tell you about how they used fecal samples (aka poop!) to learn more about the gut microbes of wild cats. But you’d have had the special treat of experiencing just that if you visited Rebecca Duhon, Tabitha Kearns and Sadie Thompson’s poster at this year’s LSU Discover Day, an undergraduate research and creativity symposium that took place in the LSU Student Union on April 4.
At LSU Discover Day 2017, 18 students enrolled in Honors 3035 with Gary King this semester presented their research on microbiomes, or the combined genetic material of the microorganisms in a particular environment, from environments across campus and Baton Rouge. Another group of students helped collect those samples for microbiome analysis. Students enrolled in Biology 2051 (General Microbiology) with Gary King and Ginger Brininstool helped sample microbes from a wide range of environments, ranging from soil at various sites around the LSU campus, to residential lawns, to BREC parks, to BR Zoo habitats, to the fecal matter of tigers and other large felids, herbivores, dogs and foxes.
The overall goal of this “Sequence the City” microbiome project, started by LSU Professor of Biological Sciences Gary King in collaboration with Biological Science Instructor Ginger Brininstool, is to engage students in sampling and analyzing the microbial communities that shape the world around us and with which we interact.
“Through their sampling and data analysis, the students develop new knowledge that we will share with the scientific community and public in a variety of ways,” Gary said. “Students not only learn about microbiomes, they also get an insider's view of science, some of its outcomes and how to communicate scientific results.”
As a part of this ongoing project, every year students enrolled in Biology 2051 extract DNA from samples they collect during the semester, such as soil samples from LSU Mike the Tiger’s habitat, the BREC Farr Park Equestrian Center, and other spots on LSU’s campus. Based on the extracted DNA samples, Gary’s students generate 16S rRNA gene sequences in collaboration with researchers at Michigan State who have access to Illumina gene sequencing machines. Students enrolled in Gary King’s microbiome analysis course, Honors 3035, then analyze these gene sequences to identify the microbes present in various samples.
In the microbiome analysis course Honors 3035, students learn the basics of "microbiome-ology," or the study of microbiomes. The students read and discuss relevant scientific papers and then analyze assigned gene sequence datasets using the bioinformatics tools they read about. Toward the end of the semester, these students present their results and findings at LSU Discover Day.
Students taking Honors 3035 this semester focused on different aspects of the larger project to Sequence the City. Undergraduate students Rebecca Duhon, Tabitha Kearns and Sadie Thompson analyzed 16S rRNA gene sequences found in fecal samples from bobcats, cougars, servals, foxes and LSU’s Mike VI to determine their gut microbiomes.
Tabitha is an undergraduate student majoring in Biological Sciences and minoring in Human Nutrition. As a pre-med student, Tabitha took Honors 3035 with an interest in getting involved more with research.
“We analyzed the most abundant genera [of microbes] and their role in digestion,” Tabitha said. “All of the species contained high amounts of Firmicutes, a type of bacteria.” The students found Clostridia in the microbiomes of these wild cats and foxes, a type of Firmicute that helps metabolize insoluble carbohydrates. They also found Bacteroides from the phylum Bacteroidetes, bile-tolerant microbes associated with diets high in meat.
“Both Clostridia and Bacteroides are indicative of a healthy gut,” Tabitha said. “Our results showed that differences in the animals' diets affected their gut microbiome composition. Bobcats, servals, cougars and tigers are hyper-carnivores. Their gut microbiomes contained more Bacteroides than foxes, which are omnivores. Besides Mike VI, all of the gut microbiomes we analyzed contained high amounts of Fusobacteria, raising questions about Fusobacteria's previous link to colon cancer.”
Microbiomes function as an ecosystem, and the study of microbiomes often involves investigating how microorganisms interact with one another and the specific environment they inhabit.
“It was surprising to learn that the composition of the gut microbiome changes with age,” Tabitha said. “As one ages, the gut microbiome contains more Bacteroidetes and fewer Firmicutes.”
Another group of students including biology major Micheline Guida focused their Honors 3035 course-based research project on the impact of fecal matter on soil microbial diversity. The group found no differences in microbial composition between soil samples based on fecal input.
“People often don’t understand what a microbiome is and how much of an impact it has on an individual’s everyday life,” Micheline said. “To me, our most unexpected finding was that in a giraffe fecal sample we found the composition of spirochetes to be 11.1%.” Some spirochetes, a type of bacteria, are symbionts that break down hard-to-digest products in the stomachs of ruminants such as giraffes. Other spirochetes are responsible for diseases such as Lyme disease.
“Through this class, I’ve realized that there are microbial communities in pretty much everything,” Micheline said. “For example, before you brush your teeth in the morning you may feel a layer of film above your teeth. This layer of film is a microbial community."
Micheline also conducts volunteer research for the Shirley C. Tucker Herbarium on campus. In her Biology 1209 lab, she performed research on plants from the Bluebonnet Swamp. “Research is something that I am very passionate about and I plan on pursuing a career in research following graduation,” Micheline said. “In my opinion research is what shapes our future.” When she isn’t doing research, Micheline is playing tennis and participating on the LSU Mock Trial Team.
Ari Saravia, an LSU student majoring in biology with plans to study medicine, says he developed a deep interest and desire to understand the role of microbiomes in human health and disease while taking Biology 2051 with Ginger Brininstool last semester.
“An ecosystem [for microorganisms] may be a meadow, a plant root, or a human gut,” Ari said. “It's interesting to study them because they can get overlooked due to their size, but they most likely play a large role in the maintenance of any ecosystem you can think of. They're also extremely diverse and are hard to classify, often leaving plenty of scientists scratching their heads, so it's an area of research that needs a lot of work. The most surprising finding from our study was realizing that we classify bacteria with a 97% similarity [in their genomes] as the same, while humans and chimps are regarded as different with 99% similarity. This shows that classifying bacteria is another ball game.” Ari is also conducting undergraduate research in Marlene Janes’ food microbiology lab in the College of Agriculture.
Through both Biology 2051 and Honors 3035, over 900 students are involved in Gary King and Ginger Brininstool’s Sequence the City project every year.
“I would definitely be interested in finding other research-based classes because research allows me to apply what I've learned in lectures!” Tabitha said.