American researchers have published the first major results of a study on the human microbiome which has seen more than 10,000 ‘citizen scientists’ from around the world mail in their poop and spit.

Based out of the University of California (UC) San Diego School of Medicine, the American Gut Project is the largest published study to date of the unique microbial communities that inhabit human bodies.

The crowdsourced, global citizen science project is designed to better understand human microbiomes: which types of bacteria live where, how many of each, and how they are influenced by diet, lifestyle and disease.

UC San Diego is a world-leader in microbiome research, driven to understanding the distinct constellations of bacteria, viruses and other microorganisms that live within and around humans, other species and the environment. Its Center for Microbiome Innovation is led by world-renowned microbiome researcher Rob Knight and 16 other UC San Diego professors from fields including medicine, engineering, pharmaceutical sciences, biological sciences, and oceanography.

Founded in 2012 by Knight as a subset of the Earth Microbiome Project, the American Gut Project study encourages citizens to contribute US$99 and receive a kit to collect a fecal, oral or skin swab and mail it back. Participants also answer a voluntary survey that includes questions about general health status, disease history, lifestyle and diet. Participants then receive a report that details what’s living in their body. As of mid-2017, the project included microbial sequence data from 15,096 samples provided by 11,336 people, primarily from the United States, Britain and Australia, along with 42 other countries or territories. “It’s really amazing that more than 10,000 people … have mailed their poop to our lab so that we can find out what makes a difference in somebody’s microbiome,” said Knight.

To tease out the identities of the bacteria living in a participant’s mixed sample, the American Gut Project team sequences a genetic marker unique to bacteria and archaea. Called 16S rRNA, this molecule acts as a sort of barcode for these microbes. For the thousands of samples, they also used metabolomics to identify the non-living molecules and chemicals.

The study found that various factors play a role in the diversity of the human gut microbiome, such as diet, the use of antibiotics or mental health. A higher number of plant types in a person’s diet led to more diversity of his or her gut microbiome; The participants who ate more than 30 plants per week also had fewer antibiotic resistance genes in their gut microbiomes than people who ate 10 or fewer plants. The team also found that people with a mental disorder had more in common with other people with mental disorders, in terms of the bacteria makeup of their gut microbiomes.

However, the researchers say most of the findings so far are simply observations or associations. The AGP is dynamic and ongoing, with all data collected publicly available (without identifying information) to allow researchers around the world to mine the data for meaningful associations between factors such as diet, exercise, lifestyle, microbial makeup and health.

At a celebration of the milestone publication on May 15, the team announced an expansion of the project called “The Microsetta Initiative”, which will serve as an umbrella for sites that can receive samples in countries around the world. Investigating more populations will provide the opportunity to see more diversity, while the living nature of the dataset will allow researchers to document global homogenization driven by increased travel, lifespans and access to similar diets and therapies, including antibiotics.

Knight said: “The analysis presented here represents a single snapshot, but we’re going to beyond making maps of the microbiome to making a microbiome GPS that tells you not just where you are on that map, but where you want to go and what to do in order to get there in terms of diet, lifestyle or medications.”


Featured image: UC San Diego professor of pediatrics and computer science and engineering Rob Knight, whose lab leads the project at the UC San Diego Center for Microbiome Innovation


(via The Nation, UCSD News, CMI UCSD