This is an article from the spring 2016 issue of LSA Magazine. Read more stories from the magazine.
LSA students in a new introductory biology lab have been taking a closer look at what might be the most compelling study subject of all—themselves. Using their own bodily bacteria, these students conduct “me”-search to take a truly hands-on approach in scientific research.
In prior centuries, scientists had to get uncomfortably close to the objects they studied—tasting plants to get a sense of how much poison was on each leaf, harassing stinging insects to prove that yes, those bugs are venomous. The tradition continues in the 21st century, as professional researchers and stay-at-home scientists continue to poke and prod themselves for the sake of discovery. The personal genetics kit 23andMe, for example, allows anyone to sequence their own genes and discover their disease risk or Neanderthal heritage. Another kit called Wisdom Panel helps pet owners unravel their mutt’s mixed breed.
Welcome to the world of “me”-search, where the “quantified self” is the most compelling subject of study, through analyzing personal data and sitting in on scientific experiments. Some LSA lab courses are running with the idea. By including stool samples in the syllabus, for example.
By dry weight, poop is 40 percent microbes—the bacteria and other tiny organisms that live inside our bodies. An accurate census is hard to pin down for the population of microbes that lives in each person, but trillions of microbes outnumber human cells and account for three pounds of an average person’s weight. Some of them harm us, but the vast majority of microbes live in our digestive system and help us process food, overcome allergies, and generally maintain our health. By analyzing their own samples, LSA students in a new intro biology lab are researching the contents of their very own gut microbiome.
Using a protocol that involves wax paper, a Popsicle stick, and several flushes, students extract DNA from their fecal samples and sequence the members of their gut microbe community. The students then link the DNA information to data about themselves: height, weight, gender, daily diet, and other relevant stats. They use those data to test hypotheses about how their gut microbiome actually affects their health: Does the microbial community differ between lean students and students with higher BMIs? Students who were breast-fed and those raised on baby formula? Students delivered by Caesarian sections and those by natural births?
Smells Like They're Learning
In lab one afternoon, students mix mouse droppings with foul-smelling ingredients. “A lot of undergrads will never get a chance to grow anything like this,” says postdoctoral fellow Jessica Sieber as she demonstrates the techniques they’ll need for rearing gut microbes in the lab. She notes that researchers don’t often culture these kinds of microbes; the work of growing them is unwieldy, not to mention stinky. Instead, labs often turn to DNA sequencing—studying microbes with computers instead of using hands-on lab techniques. But in this LSA lab, Sieber says, students gain experience with both digital analyses and practical lab work.
Lab experiments relate to the data students collect about microbes in their own bodies. For their final projects, teams of students use class data to test a hypothesis about the gut microbiome. For example: Do students' microbial communities differ based on what dorm they live in?
The goal of the mouse poop experiment is to see how different microbe species behave in different environments. Students create microcosms for the bacteria—tiny environments that are realistic but seriously scaled-down versions of a gut microbiome—giving students a peek at the workings of their own microbes. They introduce their bacteria into different microcosms and watch what happens. They’ve found that, when the bacteria are exposed to different environments, the gut microbiome’s chemical secretions differ. One of those chemicals is an anti-inflammatory that’s good for human health.
All semester, the students huddle in the lab to learn firsthand about the data they’ve collected. The syllabus steers away from more traditional “cookbook” lab courses, in which correct, expected outcomes are easy to grade.
“We want students to see the whole process of discovery, from when we don’t know the answer to when we get the answer,” says Deborah Goldberg, a professor in LSA’s Department of Ecology and Evolutionary Biology who helped spearhead new interactive lab courses on campus. “That's the real excitement of science.”
This hands-on approach will hopefully produce insights about the gut microbiome that can have an impact beyond the classroom. Maybe the “me”-search of labs like this one can turn outward to improve public health for people around the world.
That’s the big plan. More labs in LSA have followed this practical research model, with students building solar cells to figure out how to improve renewable technology or scooping snow from the highway to see how road salting can change environmental chemistry. And faculty from across campus, collectively known as the Michigan Microbiome Project, aim to link microbial communities to other pressing public health concerns, like obesity, mental illness, and harmful algal blooms in the Great Lakes. Michigan Microbiome Project faculty, including Professor Tom Schmidt (B.S. ’78)—who helped launch the gut microbiome lab—will compile the student data from these intro biology labs and share their results with the broader scientific community.
Really, this work is just beginning. Microbes are difficult to identify as species, let alone understand as communities, and we know little about their specific functions. “I feel like we're actually at the start of something big,” says Andrew Stevens as he injects microbes into a test tube. He’s an undergrad who’s planning on a career in psychiatry or alternative medicine. “When we first discovered DNA, people didn’t realize that it would be useful for anything like identifying things at crime scenes. As we research the microbiome more, we’re going to realize its effects and that we can manipulate it. We’re going to be able to actually affect the microbiome, and affect our body as a result.”
“Knowing I contributed to that in some way,” adds another student working at the lab bench, “is pretty cool.”
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