We are what we eat: The American Gut Project

June 12, 2018

Our inner lives—from digestion to mental health—are affected by the bacteria that live in our guts, based on the first major findings of a study of the “poop” of 11,336 average Joes by researchers at the University of California San Diego School of Medicine and their collaborators worldwide. The American Gut Project, launched in November 2012, is a crowd-sourced, global citizen science effort 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.

The project—described May 15 in mSystems, the journal of the American Society for Microbiology— is the largest published study to date of the human microbiome.

“It’s really amazing that more than 10,000 people—members of the public who want to get involved in science whether or not they work in a lab or have a [doctoral degree]—have mailed their poop to our lab so that we can find out what makes a difference in somebody’s microbiome,” said Rob Knight, Ph.D., who is one of three co-founders of the research project and who also is a professor in the UC San Diego School of Medicine and Jacobs School of Engineering, and director of the Center for Microbiome Innovation at UC San Diego.  The other two are Jeff Leach, Ph.D. and Jack Gilbert, Ph.D.

The researchers recruited their participants—mostly from the United States, the United Kingdom, and Australia, but also from 42 other nations and territories—who were willing to contribute $99 as “citizen scientists.” Having done so, they then received a kit, which enabled them to collect a fecal, oral, or skin swab and then mail it back to UC-San Diego. Along with the sample, each participant answered a voluntary survey that included questions about general health status, disease history, lifestyle, and diet. They also could choose to participate in an online forum called Gut Instinct, through which they could share their lifestyle-based insights. Once the sample was processed, participants received a report that detailed specifically what was living in their guts (or other body site).

To tease out the identities of the bacteria living in a participant’s mixed sample, the American Gut Project team sequenced a genetic marker unique to bacteria and archaea. Called 16S rRNA, this molecule acts as a sort-of bar code for these microbes.

First findings

All of the data collected by the American Gut Project are publicly available, without participants’ identifying information. This open access approach allows researchers around the world to mine the data for meaningful associations between factors such as diet, exercise, lifestyle, microbial makeup and health. Among the observations that have emerged to date are the following:

  • Diet: The number of plant types in a person’s diet plays a role in the diversity of his or her gut microbiome—the number of different types of bacteria living there. No matter the diet they ate, participants who ate more than 30 different plant types per week (41 people) had gut microbiomes that were more diverse than those who ate 10 or fewer types of plants per week (44 people). The gut samples of these two groups also differed in the types of molecules present.
  • Antibiotics. The gut microbiomes of American Gut Project participants who reported that they took antibiotics in the past month (139 people) were, as predicted, less diverse than those of people who reported that they had not taken antibiotics in the last year (117 people). But, paradoxically, people who had taken antibiotics recently had significantly greater diversity in the types of chemicals in their gut samples than those who had not taken antibiotics in the past year. What’s more, 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. In other words, the bacteria living in the guts of the plant-lovers had fewer genes that encode the molecular pumps that help the bacteria avoid antibiotics. This study didn’t address why this might be the case, but the researchers think it could be because people who eat fewer plants may instead be eating more meat from antibiotic-treated animals or processed foods with antibiotics added as a preservative, which may favor the survival of antibiotic-resistant bacteria.
  • Mental health. The American Gut Project researchers also examined the gut microbiomes of 125 people who reported having a mental health disorder, such as depression, schizophrenia, post-traumatic stress disorder (PTSD),or bipolar disorder. They matched each of these participants to individuals who did not have a mental health disorder, but did have other major factors in common, such as country, age, gender, and body mass index. The team 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, than they did with their mentally healthy pairs. The observation held true in both U.S. and U.K. populations, in males and females, and across age groups. In addition, the research team found some indications that specific bacteria types may be more common in people with depression than people who do not have the condition.

Most of the findings emerging from the American Gut Project so far are simply observations or associations, and in many cases researchers can’t yet extrapolate the ultimate effect on human health. For example, while the researchers observed that people who eat many plants have a more diverse gut microbiome than those who don’t, they don’t yet know if increasing a person’s microbial diversity from its current level would have a direct positive effect on his or her health. However, the ultimate goal is to improve health with this knowledge.

 The work is ongoing. “The human microbiome is complex, but the more samples we get, the sooner we will be able to unravel the many ways the microbiome is associated with various health and disease states,” Knight said. “The American Gut Project is dynamic, with samples arriving from around the world daily. The analysis presented in this paper represents a single snapshot, but we want eventually to go 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.”

To participate in the American Gut Project, visit AmericanGut.org 

Research contact: hbuschman@ucsd.edu

Leave a Reply

Your email address will not be published. Required fields are marked *