The first results of the largest study to have ever investigated the human microbiome are in. They have important implications for our dietary practices, resistance to antibiotics, and our mental health.
In 2012, Rob Knight, Ph.D., from the University of California (UC), San Diego, Jeff Leach, Ph.D., the founder of the Human Food Project, and Jack Gilbert, Ph.D., who is the faculty director of the Microbiome Center at the University of Chicago in Illinois, set out to found the American Gut Project.
The aim of the project was to learn more about the human microbiome — that is, the collection of genes that encode all of our microbes.
Specifically, the researchers wanted to know how many types of bacteria live in our bodies and where, and how our diet and lifestyle affect the composition of these microbes.
To this end, they used so-called citizen science — the practice in which the public contributes to research by offering their time and personal data up for analysis.
The first results of the project are now available, and they offer clues as to what keeps our guts healthy and bacterially diverse. The findings were published in the journal mSystems.
As part of the project, participants paid $99 for a kit that collected fecal, oral, and skin samples of bacteria.
They also had to answer a survey inquiring about their overall health and any illnesses they might have had, their lifestyle, and dietary practices.
In 2015, the project counted 15,096 samples provided by 11,336 people across the United States, United Kingdom, Australia, and 42 other countries.
The researchers then used genomic sequencing to analyze a genetic marker called 16S rRNA, a molecule unique to bacteria.
They also studied the set of metabolites in the samples, in order to analyze other molecules and chemical compounds that might be present.
Finally, the scientists used a method called shotgun metagenomics — which is an innovative and powerful DNA sequencing method — to comprehensively analyze the genetic data.
First, the results suggest that a more diverse plant-based diet makes for a more bacterially diverse gut.
Specifically, those who consumed more than 30 different types of plant each week had much more diverse microbiomes than those who consumed only 10 or fewer types of plant weekly.
However, the researchers note that these results do not necessarily mean that increasing microbial diversity is a positive thing for someone’s health.
Secondly, the participants who reported eating more than 30 types of plant per week seemed to have a lower resistance to antibiotics.
The researchers found fewer genes indicating antibiotic resistance in the fecal samples of these people — that is, fewer genes that help the bacteria to escape the drugs.
While the study is purely observational and could not conclude anything about causality, the authors speculate that individuals whose diets contain fewer plants could be compensating with eating either meat — which may have been treated with antibiotics — or processed foods that have had antibiotics added to them.
Finally, the study revealed interesting connections between the composition of the gut’s bacteria and mental illness.
Those who reported living with post-traumatic stress disorder (PTSD), schizophrenia, depression, or bipolar disorder were compared with healthy controls who had been matched for age, gender, and body mass index (BMI).
The results demonstrated that people who reported mental health issues had more bacteria in common with other people who reported similar problems than they did with the controls.
This association was strong regardless of gender, age, or geographical location. Also, the research suggests that some types of bacteria may be more prevalent in people who live with depression.
These findings strengthen the link drawn between mental health and gut bacteria by previous research.
Daniel McDonald, Ph.D., the scientific director of the American Gut Project at UC San Diego School of Medicine, weighs in on the significance of the findings. He says:
“We observed a much greater microbial diversity than previous smaller studies found, and that suggests that if we look at more populations, we’ll see more diversity, which is important for defining the boundaries of the human microbiome.”
Knight holds a similar sentiment, saying, “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.”
“The American Gut Project is dynamic, with samples arriving from around the world daily,” Knight adds.
“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.”
Rob Knight, Ph.D.