The Student Microbiome Project

The Student Microbiome Project 470
Dr. Caporaso and students. Photo: Monica Saaty, IDEA Lab.

“You may or may not know, but there are 10 times as many bacterial cells that live in your body as there are human cells,” says Greg Caporaso, Assistant Professor in Biology and Computer Science at Northern Arizona University (NAU). As humans, we are engaged in a symbiotic relationship with communities of microbes—literally trillions of microorganisms that live in and on our bodies. They provide some benefits to us, such as helping us extract nutrients from food, and, in return, we provide a warm, wet place for them to live and thrive.

Caporaso and his team of researchers are working on “The Student Microbiome Project” in collaboration with Rob Dunn at North Carolina State and Noah Fierer at the University of Colorado at Boulder. They are examining microbial communities on and in the bodies of 100 student volunteers. 

New technologies enable us to study the human microbiome

Research on the human microbiome, these communities of microbes in and on our bodies, has seen rapid advances over the past 10 years, largely driven by the vast decrease in the cost of sequencing DNA. “We are just now at the point where we are starting to understand the associations between the microbiome and various disease states in which we are interested,” says Caporaso. For example, at Washington University, in Jeff Gordon’s lab, researchers are able to show an association in mice—that appears to be the same in humans—between the microorganisms that are living in their gut and whether they are obese or at a healthy weight. “So this research holds the potential to help treat conditions like obesity by altering the microorganisms living in our bodies,” says Caporaso. “This is what we are involved in exploring.”

The Student Microbiome Project is assessing the temporal variability in the microbiome across a number of different individuals. Every week for 10 weeks, students donated samples from different body sites: the palm of their hand, their forehead, their tongue, and their gut (by swabbing used toilet paper). This provides a minimally invasive way for researchers to investigate the microbial communities living in and on these volunteers. 

“This is the first time we have technology to study the human microbiome in such great detail,” says Caporaso. “It’s great to be in this field [human microbiomics] at this time.” 

At the start of the project the students were given a 50-question questionnaire that asked about their diet, their living situation, how long they have lived in their current residence, and so on. Every week thereafter, the students were asked to update any changes in their diet or health and to report anything else that might have happened that could have disturbed their microbial communities. Caporaso watched that information closely. “One of my main motivations for the project is to understand what constitutes a disturbance to a human-associated microbial community,” he says. “While we know that taking things like antibiotics and getting sick or changing one’s diet can have an effect on microbiomes at least in theory, we want to understand which one of those changes actually has an effect on a microbiome and to figure out if we can quantify those disturbances.”

The data set is unique in addressing these kinds of questions, as it is the first time temporal data has been collected from this many individuals at this many body sites. Over 100 gigabytes of data has been generated as part of this study, mostly in the form of DNA sequences. This is where Caporaso’s expertise in bioinformatics comes into play.

Student participants involved in research

Another interesting aspect of the project is that not only are students the subjects of the study but many are also participating in independent research alongside Caporaso, developing and applying bioinformatics software to analyze the data. Even if they are not directly involved in examining the results, participating students get their personal microbiome information delivered back to them and can compare their own personal microbial community with that of other study participants. Study participants received a summary of their microbial communities, which was delivered to them using the MyMicrobes system developed by John Chase and Jai Ram Rideout in the Caporaso Lab. An example of the data that students received can be found at http://my-microbes.qiime.org. “This project was a fun way to get my bioinformatics students excited about microbiology by actually involving them in research. I think that is really cool because we take student data and feed it back into our classes,” says Caporaso.

The data sets from The Student Microbiome Project are currently being analyzed, and the results will be submitted for publication in the upcoming months. Being able to study these microbial communities and turn the data into useful information that can be translated into clinical practice holds the potential to alter various disease states and also intimately change the way we interact with our bodies. “This is the first time we have technology to study the human microbiome in such great detail,” says Caporaso. “It’s great to be in this field [human microbiomics] at this time. 

--Kelly Zarcone