Let’s say you’re an average, healthy adult. Right now your body is teeming with bacteria—tens of trillions. Some scientific estimates say the bacteria inside you outnumber your own cells ten to one.
This is normal, though. These microbes may even deserve some of the credit for your good health. A nice variety of bacteria in your gut, for example, has been linked to a reduced risk of diabetes, obesity, and asthma.
The microorganisms in our environment are almost as much a part of us as our own cells, yet scientists have still only studied a tiny fraction of them. As abundant as they are in our bodies, the water we drink, and the air we breathe, less than one percent of bacteria can be cultured for closer study in a laboratory environment.
Creighton Friend hopes to help change all that. A fourth year biology student, he’s spending his summer learning about a new branch of science called metagenomics, which allows researchers to capture a complete “snapshot” of all the organisms in an ecosystem from small environmental samples. This emerging field is the focus of a new honors program at the Biocomplexity Institute of Virginia Tech.
“I want my career to be about protecting people from infectious disease, but you can’t fight what you can’t see,” said Creighton. “With new genetic sequencing technology, our awareness of the microorganisms all around us is starting to expand dramatically—I think it’s my responsibility as a future scientist to learn how to use that knowledge for the greater good.”
Excited as students like Creighton might be to get hands-on experience in this new field, the highly specialized equipment required to perform metagenomic research isn’t always easily accessible. Fortunately for Virginia Tech undergraduates, the Biocomplexity Institute is home to the Genomics Sequencing Center (GSC), a state-of-the-art biological data analysis facility that serves over twenty academic departments on campus, as well as international research collaborators and a range corporate partners.
Virginia Tech’s Amy Pruden and Marc Edwards have taken advantage of this unique resource in their ongoing investigation of contaminants in water and other environmental sources. Undergraduates studying in the GSC this summer will learn to process environmental samples, monitoring for dangerous Legionella bacteria, which were recently found to be prevalent in cities’ heated water systems.
“Our students came to this course extremely dedicated in an academic sense, but the importance of their work and its potential impact in helping communities that are already at risk has taken their motivation to a new level,” said Saikumar Karyala, a GSC research scientist and Metagenomics Program instructor.
The important work being done at the GSC recently garnered the support of Thermo Fisher, an industry leader in scientific technology development. In 2016, the company donated their Ion Torrent S5 genomic sequencer to the center, cutting-edge equipment worth more than $160,000.
“The Ion Torrent platform is transforming the way we use targeted sequencing to identify the organisms that are present in environmental samples,” said Shiv Kale, a Biocomplexity Institute research scientist and lead instructor of the Summer Metagenomics Program. “These students are getting a truly unique, hands-on opportunity, utilizing both novel methods and technologies to dissect these environmental samples.”
Distinctive resources like these have allowed the Biocomplexity Institute to develop a range of academic programs, training students in topics from data science to systems biology.
“For students getting their start in the sciences, you really can’t overstate the importance of a hands-on learning experiences like this,” said Biocomplexity Institute Director Chris Barrett. “When they leave our labs they’ll know how genetic sequencing is done, they’ll understand how the information they see in studies relates to problems in the real world, and they’ll be prepared to communicate the importance of this work to their friends and future colleagues.”
Students like Creighton Friend agree. He and his classmates in the inaugural Summer Metagenomics Program will present the results of their original research projects at a public reception, to be held at the Biocomplexity Institute on August 11.
“As a fourth-year student in the sciences, I’m already preparing for the next step up in my education,” said Creighton. “This has been an awesome opportunity for me to grow my knowledge and set my priorities as a researcher moving forward.”
Editor's Note: The students enrolled in this summer’s metagenomics program include Zachary Barron, an Environmental Science major; Erod Baybay, a Physics major with a minor in Mathematics and Computer Science; Clark Cucinell, an Honors College major in Computer Science and Chemistry; Alexandra Cummings, a Computational Neuroscience major; Creighton Friend a Biochemistry, Nanoscience and Microbiology major with a minor in Chemistry and Biology; McKaella Grow, an Honors College major in Human Nutrition, Foods and Exercise; Nicholas Stancil an Honors College major in Human Nutrition, Foods and Exercise with a minor in Chemistry.