In 2018, 11,336 American Gut participants mailed samples from used toilet paper to scientists; the dataset characterized microbial diversity on an unprecedented scale

In 2018, 11,336 people in the United States, the United Kingdom, and dozens of other countries mailed in swabs taken from used toilet paper as part of that research effort. "American Gut" is the project's official name, even though its participant base was international. That batch of 15,096 samples became the largest publicly available dataset on the human gut microbiome at the time, and it found far more bacterial diversity than any smaller study had before, according to the University of California San Diego. According to the University of California San Diego, which ran the Center for Microbiome Innovation project, the findings were published in the open-access journal mSystems in May 2018 in a paper that still survives in the National Institutes of Health's National Library of Medicine.

This was not a small clinical trial run on a few dozen volunteers. Thousands of ordinary people, including science writer Michael Pollan, paid a $99 kit fee, filled out a survey on their diet, health history, and lifestyle, and mailed their sample to a lab: no doctor's referral, no hospital visit.

How a mail-in swab became a research project


Participation required only a $99 kit and a willingness to provide a sample and help catalog microbial life across environments. Participants took a sample of their choosing, answered a few demographic questions, and sent it to a lab (UC San Diego for U.S. residents, King's College London for the U.K., or the University of Queensland for Australian residents). The researchers then sequenced the 16S rRNA gene to identify which bacteria and archaea were present, and for thousands of samples they also used metabolomics and shotgun metagenomics to find out which molecules and genes were there. Daniel McDonald, the project's scientific director, said they found a wide range of diversity in human microbiomes, suggesting that sampling more people may reveal more about what constitutes a healthy microbiome.

Variety beat quantity when it came to plants

Eating more vegetables was not the deciding factor. Consuming more types of plants was. Among 41 participants who ate more than 30 plant varieties per week, gut microbiomes were more diverse than among the 44 participants who ate 10 or fewer. These two groups were smaller subsets of the larger 11,336-person dataset, not the full sample. The other two groups also showed differences in the molecules detected in their samples. This result corresponds to separate research on dietary fiber; a peer-reviewed review study, "Dietary Fiber Intake and Gut Microbiota in Human Health," published by the National Institutes of Health's National Library of Medicine, found that individuals on fiber-rich diets consistently carry a different mix of gut bacteria than individuals who consume less fiber.

Antibiotics behaved as expected, until one number flipped

As expected, gut bacterial diversity decreased among participants who had recently taken antibiotics. 139 participants had taken antibiotics in the last month, and 117 had not taken them in a year. However, the chemical profiles showed the reverse pattern. Participants who had taken antibiotics in the last month showed more diverse chemical profiles in their samples. The study authors also noted separate variation in antibiotic-resistance markers between the two plant-diversity groups, though the analysis focused on microbiome diversity and diet rather than establishing a direct causal link between plant variety and antibiotic resistance.

Two strangers can share a gut profile if they share a diagnosis

On their own, age, country, and body weight were not strongly linked to similar gut profiles, so researchers controlled for them separately when isolating the effect of diagnosis. For the study, researchers followed up with 125 participants who reported a diagnosis of depression, PTSD, bipolar disorder, schizophrenia, or another mental illness. Each was matched with a similar-age, same-country-of-birth, and similar body mass index participant without a mental health diagnosis. Participants with mental health diagnoses had more similar gut bacteria to one another than to their matched healthy counterparts. This pattern held for both the United States and U.K. samples across sexes and ages.

A surgery dramatically changed one participant's gut microbiome

A single surgery dramatically altered one man's gut microbiome, more than a decade of normal living. UC San Diego computer science professor Larry Smarr sampled his own intestines repeatedly before and after colorectal surgery. Researchers found that his gut microbiome changed after the operation, and his post-surgery samples were more similar to those of intensive care unit patients than to his earlier samples. McDonald observed that the difference between Smarr's pre- and post-surgery samples was about as large as the difference between marine sediment and soil beneath a plant. He noted that even extreme diets rarely cause changes this dramatic; surgery does.

The takeaway for your grocery list, not your mailbox

Buying a $99 test kit is not what any of this is about. The broader point may be that people can make changes in their 20s or 30s, such as varying their diet rather than eating huge portions of the same foods. Along those lines, the researchers suggested that eating a wide range of fruits and vegetables, whole grains, legumes, and nuts may support gut health. The dataset they used has grown exponentially in recent years as part of the Microsetta Initiative, an ongoing citizen science project, and they expect it to get even bigger. They plan to update their findings regularly as the dataset grows and their understanding of a healthy microbiome improves.