These researchers would like you to mail them your gut bacteria

Thousands of participants have submitted swabs of their feces to the American Gut Project

Most of the DNA in your body isn’t yours; it belongs to the bacteria that comprise your personal microbiome. This bacterial make-up has significant health implications, but which factors determine our gut bacteria, and how the microbiome in turn impacts our heath, is not yet fully understood. That will require a lot of data, and the American Gut Project has come up with a novel way to collect it: a participant-funded citizen science program, through which thousands of volunteers have already mailed in samples of their gut, mouth, or skin microbiomes. Researchers Embriette Hyde and Rob Knight tell us more. 

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ResearchGate: What is the American Gut Project?

Embriette Hyde and Rob Knight: The American Gut Project is one of the largest crowdsourced citizen science projects in existence today. Established late 2012, the goal of the project is to build a comprehensive map of the human microbiome, enabling researchers to identify bad and good areas on the map, and promote research to determine how to move people from the bad to the good areas. We are open to anyone in the world, and our 8500+ participants have sent us over 10,000 samples and contributed nearly $2 million to cover the cost of processing, sequencing, and analyzing those samples. We are completely open source, which means that all of our protocols for sample processing, sequencing, and analysis, as well as the data, are open and freely available to anyone. Participants know exactly what we've done with their sample and can dig deeper into their data if they want, and a handful have. Other research groups can also access the data and use it in their own research.

RG: How did you come up with this idea?

Hyde and Knight: In 2012, Jeff Leach approached me with the idea that we could open up some of the tools developed for the Human Microbiome Project to anyone who was interested. I thought it was a crazy idea, but not so crazy that we shouldn’t try it out. And clearly, in retrospect we’re all glad that we did! The project has greatly enhanced the public’s ability to participate in human microbiome science.

“If we want to improve human health, we need to treat humans as the supraorganism that they are, and determine how our microbiomes interact with us”

RG: Why is it important to collect data on gut microbiomes?

Hyde and Knight: If you compare the number of genes encoded by your own human DNA to the number of genes encoded by the DNA of the microbes that live in your gut, you'll quickly realize that you are a supraorganism carrying only about one percent human genetic information and 99 percent microbial genetic information. Those microbial gene products are not sitting by silently. In fact, we know they do really important things for us, such as break down plant polysaccharides that our human cells cannot, produce vitamins that we can't get from our diet, inform appropriate maturation of our immune system, and fight off pathogens. In the past decade, dozens of research groups have identified associations between the gut microbiome and countless health and disease states from inflammatory bowel disease to obesity to autism. If we want to improve human health, we need to treat humans as the supraorganism that they are, and determine how our microbiomes interact with us in health and disease.

RG: What exactly happens with the samples when you get them?

Hyde and Knight: When the samples arrive in the lab, we scan the barcode on the sample tube, which will tell us if the participant has signed their consent form and completed all of the required steps for us to begin sample processing. If all is good, one of the swab tips is then cut off with sterile scissors into a 96-well plate containing other samples—one sample per well. This plate is then stored at -20C to protect the sample. Once 90 samples are on the plate—the other wells are "blanks" to ensure our process is clean and accurate—the plate is passed off to a liquid handling robot that adds in buffers and other formulations for extracting the DNA from the sample. We then use polymerase chain reaction (PCR) to amplify a region of the bacterial 16S rRNA gene (variable region 4), which enables us to profile the bacterial community present. These "amplicons" are then sequenced, and after sequencing, run through a series of computational steps to provide us-and the participants-with information about what is in the sample. We quality control the sequences to ensure only the highest quality sequences are included in the analyses, and then align those sequences against a reference database, which enables us to taxonomically classify the different bacteria present in the sample. We can then apply several statistical and visualization techniques to compare samples to one another and look for connections between the bacterial community and, say, diet type or disease state.

“The sample collection itself isn't hard, and if someone has done it wrong, we can tell when we see the data.”

RG: What have you learned so far? Any surprises?

Hyde and Knight: Some of the strongest associations are with the country you live in, the number of types of plants you eat in a typical week, and how much sleep you get each night. We've also noticed that exercise frequency, alcohol consumption, and the number of bowel movements one makes in a day are also linked to microbiome diversity.

RG: How does the fact that these samples were collected at home by untrained participants affect your ability to use the resulting data?

Hyde and Knight: One of the biggest factors affecting samples is the fact that some bacteria do grow while the sample is in the mail. We have compared American Gut samples to several quality control and storage condition microbiome studies to identify the bacteria that grow in transit. We then remove those sequences from every sample before we move forward with analysis and produce results.

The sample collection itself isn't hard, and if someone has done it wrong (i.e. put the swab between their butt-cheeks instead of swabbing used toilet paper as instructed) we can tell when we see the data. The other factor that we have to deal with is the honesty of our participants because all of the data are self-reported. For example, we either see a link between the microbiome and exercise, or between the microbiome and lying about exercise. We hope to resolve this by working with athletes who are more closely monitored. We can try to validate some of the answers, for example by using the Food Frequency Questionnaire that participants can opt to complete.

“Some people seriously take on the citizen scientist role and want to do all they can to help move our research forward. Others are just curious about what is living inside of them.”

RG: What do you think motivates people to participate?

Hyde and Knight: I believe the motivations are varied. Some people seriously take on the citizen scientist role and want to do all they can to help move our research forward. Others are just curious about what is living inside of them. Many have a serious disease and therefore are incredibly personally motivated to help scientists learn new things about that disease that may help find a treatment. Regardless of the motivation, all of our participants are helping us to achieve the same goal, and the project is a success because of their support and enthusiasm.

RG: How does the American Gut Project differ from other investigations of the human microbiome?

Hyde and Knight: American Gut is different from other microbiome research studies both in terms of operation and scope. Because it is crowdsourced citizen science, there is no official government funding directly associated with the project. While some collaborators have clinched grant money to support microbiome sequencing of their participants and we can receive charitable donations, the vast majority of monies come from the participants themselves. We also immediately release the data as soon as we have them. This is unique because most research data are not made available until after a publication is released. We are also one of the largest, if not the largest, human microbiome study in existence with over 10,000 samples from over 8500 people living in 35 countries!

RG: What are your plans moving forward?

Hyde and Knight: We will continue collecting samples until interest wanes, which we don't anticipate happening in the near future. We're working toward expanding our geographical reach even further by establishing additional aggregation sites in other countries. We're also nurturing current collaborations and building new ones to reach out to specific cohorts, such as student athletes, people suffering from inflammatory bowel diseases, fermented foods consumers, cancer patients, and babies and their nurses, among many others. The microbiome has some type of association with nearly every health and disease state that you can imagine, and we'd love for American Gut to be instrumental in furthering microbiome research in as many of those states as possible! It’s important for people to remember that at the moment, microbiome analysis is still very much research. Some day we hope it will lead to FDA-approved tests for specific diseases, and our participants are helping bring that day closer.

Featured image: Microbiome data on display. Credit: UC San Diego