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American Gut Project Expands to Asia

Crowdsourced microbiome sequencing effort seeks participant diversity

June 02, 2016  |  

University of California San Diego School of Medicine researchers are expanding the American Gut Project into Asia. The goal of American Gut, the world’s largest crowdfunded citizen science project, is to sequence as many human microbiomes — the unique collection of bacteria and other microbes that live in and on us — as possible.

American Gut Project participants are “citizen scientists.” They learn how many of which types of bacteria inhabit their bodies, and in doing so also contribute valuable data to researchers around the world who want to know how microbiomes influence human and environmental health.

Embriette Hyde

Embriette Hyde, PhD, demonstrates sampling with an American Gut Project kit.

“We’re excited to engage with more participants outside the US, Australia and the UK because we’re finding that, thanks to differences in diet, lifestyle and environment, the country you live in may greatly influence the microbial makeup of your gut and other body sites,” said Embriette Hyde, PhD, assistant project scientist and project manager of American Gut in the UC San Diego School of Medicine.

The American Gut Project was co-founded by Rob Knight, PhD, professor of pediatrics and computer science and engineering and director of the Center for Microbiome Innovation at UC San Diego. American Gut, British Gut, Australian Gut, and now Asian Gut are part of the Earth Microbiome Project, a massive effort to analyze microbial communities across the globe. The American Gut Project is also a participant in the White House’s newly created National Microbiome Initiative.

So far, American Gut Project results have reported that, in general, a healthy gut microbiome is one with a diverse number of bacterial species in it. Some of the things that are associated with a diverse gut microbiome are some of the same things you already know are good for your health, like a diet high in a variety of different vegetables, fruits and other plants. But there are some surprises, too. For example, microbiome diversity seems to change with time of year and even increases with the amount of sleep an individual gets each night. In the future, researchers believe a microbiome readout might help them better understand a lot about a person’s health, risk of disease and how best to treat it.

Previously, the American Gut Project could technically accept samples provided by participants anywhere in the world. But logistics were another matter. The costs to ship out a single sampling kit and then for the participant to ship it back to San Diego were prohibitive.

That’s when Scott Savage, an operations manager, and his wife, Louise Savage, a microbiologist, offered to help. The couple lives in Singapore and they have volunteered to run a local aggregation site for the American Gut Project, under the name Asian Gut. This means they will store American Gut sampling kits locally, mail them to participants in Singapore and throughout Asia, collect and store returned samples in a freezer, and then ship the kits back to San Diego in bulk. These are the same logistics as those followed in the UK (British Gut) and Australia (Australian Gut), which served as blueprint aggregation sites for this newest venture.

“We decided to get involved with the American Gut Project after watching Rob Knight’s TED talk,” Scott Savage said. “The more we researched the area after that, the more interested we became. We soon realized that gut health was central to many Asian customs. It was clear that American Gut was leading the Western approach of DNA sequencing in an open and community-driven way, so we wanted to help bridge that gap.”

American Gut

How the American Gut Project works

Carine Bonnard, PhD, a scientific project manager, is also helping Savage to collect Asian samples. “I have been studying the human genome for the past 18 years and have been particularly interested in how variations in our genes cause human diseases. When Scott spoke to me about this project, I was very interested to learn more about the ‘other’ cells that populate our body. Since there are trillions of bacterial cells living among human cells, they have to play essential role in our physiology and our health. Host genetic variations certainly influence the composition of our gut, but I am also curious to know whether the hot and humid climate in Singapore, as well as the spicy food available in Asia, have shaped my microbiome after 13 years here.”

According to Hyde, one reason the team is particularly interested in getting more microbial data from Asian participants is because people in Asian countries tend to eat more fermented food than people in Western countries. In a recent pilot study with the 2016 San Diego Fermentation Festival, Hyde and team found that people who make and eat more fermented foods had greater species diversity in their gut microbiomes than non-fermenters.

To that end, the American Gut Project has also added new questions to the survey that each participant completes. These questions are aimed at drilling down on the specific types and quantities of fermented foods a participant makes or eats — kefir, kimchi or sauerkraut, for example.

“Lots of people around the world are getting excited about microbiomes and what their makeup might mean for our health, and although the research is still in its infancy, many people want to make microbiome information actionable,” Hyde said. “We have to be careful not to put the cart before the horse, though. For example, researchers in Israel created an algorithm to help you determine what you should or shouldn’t eat based on your microbiome. It was an elegant study, but that work was only done in a very narrow population of people who live in Israel. We don’t know yet if that’s applicable to other populations. That’s why we need to expand our microbiome data collection efforts into Asia and other regions of the world.”

To learn more or participate:

  • Visit
  • Stop by the American Gut Project booth June 3 and 4 at the San Diego Rock ‘n’ Roll Marathon expo at the San Diego Convention Center

Media Contact

Heather Buschman, PhD

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