In 2009, Eric Alm, a professor of biological engineering at the Massachusetts Institute of Technology, hadn’t had a bowel movement at home for almost the entire year. Neither did Lawrence David, Alm’s graduate student at the time. Instead, every time they had to go, they’d drive to their MIT lab. There they’d take a white plastic device out of a sealed sterile bag and place it over the lab toilet. Medics call the device a hat because it looks like one—its brims keep it on the toilet sides while the sample is being deposited into it. And so for a year, the duo deposited samples, which they scooped into 15-milliliter test tubes and stored in the fridge.
Alm and David had set off to track how their daily activities changed their microbiome—the bacterial community inside the gastrointestinal tract. As the Human Microbiome Project found, our gut is a rich ecosystem teeming with hundreds of species that help us digest food and protect us from harmful germs. Yet, exactly what they are and what they do is largely unknown—in part because their lives are hard to study. “Most of them we know nothing about,” says Alm, who is also a co-founder of a stool bank named OpenBiome. “We just don’t know much about the functional role of any of these bugs.”
The only window into our mysterious inner menagerie is poop. And that’s not an easy thing to track.
“I vividly remember the first time I did it because it smelled really bad,” David, now an assistant professor of molecular genetics and microbiology at Duke University, says about the sample collection process. “I didn’t think I was going to make it through the full year after the first day—I almost threw up.” Eventually he got used to the smells, but the endeavor was far from easy. “It was tiring,” he says.
The reign of smart technology coupled with the decreasing cost of DNA sequencing used to identify the microbes made this Magic School Bus venture possible. Using a tracking app called TapForm, which David customized for the project, the duo recorded everything they did and ate every day plus their weight and moods. “The idea was that you were going to carry [the iPad] with you all day and enter things you were doing into it as you were doing them because otherwise you could forget what you did,” David recalls, adding that their records were very detailed. “It was like, I ate a salad with a slice of tomato in it and some ham, and a bag of chips.” In essence, they wanted to capture everything that went in and everything that came out. At the end, they batch-processed over 700 samples, spent another year analyzing data, and finally published their findings in the Journal of Genome Biology this summer.
Alm and David discovered that their microbiomes were comprised of different bacterial species, but remained fairly stable on a day to day basis. Eating yogurt, which contain Bifidobacteriales, unsurprisingly increased those species. Eating fiber-rich foods increased Bifidobacteria, Roseburia, and Eubacterium rectale species, known to thrive on fiber. But while the pair’s microbial communities were generally stable over the course of the year, a handful of distinct activities changed their findings quickly and profoundly.