Crowdsourcing Reveals Links Between Our Guts and Our Health

An Arivale Hot Topic

Niha Zubair, Arivale Clinical Research Scientist, PhD
Niha Zubair
Arivale Clinical Research Scientist, PhD

[Arivale Hot Topics address health stories currently in the news. The Arivale Clinical Team’s commentary on these news articles is not a review of the scientific evidence, nor an endorsement of a specific study, and is not meant as official medical opinion.]

The human microbiome – the collection of bacteria, fungi, and archaea found in and on our bodies – plays a fundamental role in health and disease.

While many studies link microbiome composition to disease states or other traits, there’s a lack of understanding of the breadth of bacterial diversity within the human population and the relative importance of lifestyle, health conditions, and diet on the human microbiome.

To increase that understanding, the American Gut project – based out of the University of California, San Diego – got underway in 2012. It’s the world’s largest crowdsourced microbiome research project, and its goal is to collect a large set of data on the human microbiome to help make advances in our understanding of the microbiome and health.

While “gut” is in the name of the project, samples are also collected from the skin and oral sites of the human body, both of which contain microbes.

The American Gut project

Last month, researchers published the first results from this crowdsourced, global, citizen science project based on samples from over 10,000 participants. In these early results, which were covered by the Daily Beast, researchers compared gut microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples.

In addition to providing fecal samples, each participant in the project answered a voluntary survey that included questions about general health status, health history, lifestyle, and diet.

The following are some of the key associations researchers observed between the gut microbiome and health.


In terms of diet, a greater number of plant types consumed correlated with an increased gut microbiome diversity (the number of different types of bacteria living in the gut). Greater microbiome diversity may be beneficial for human health.

Interestingly, no matter what diet an individual followed (vegetarian, vegan, etc.), participants who ate more than 30 different plant types per week had gut microbiomes that were more diverse than those who ate 10 or fewer types of plants per week.


The gut microbiomes of participants who reported taking antibiotics in the past month were less diverse than people who reported they had not taken antibiotics in the last year.

But, surprisingly, 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.

Antibiotic resistance genes

Individuals who consumed 10 or fewer plants types per week had a significantly higher abundance of antibiotic resistance genes in their gut microbiomes than those who consumed more than 30 types of plants per week.

One possible explanation for this is that those who eat fewer plants may be eating more meat from antibiotic-treated animals or foods with antibiotics added, which may support the survival of antibiotic-resistant bacteria – though that is only speculation at this point.

Mental health disorders

Researchers also examined the gut microbiomes of 125 people who reported having a mental health disorder, such as depression, schizophrenia, PTSD, or bipolar disorder. They matched each of these participants to “healthy” participants with other factors in common, such as country, age, sex, and BMI.

Interestingly, researchers found that those with a mental health disorder had more in common with other people with mental health disorders, in terms of the bacteria makeup of their gut microbiomes, than they did with their mentally healthy counterparts.

Arivale responds

Gut health is very important to one’s overall health and wellbeing. However, research on the gut microbiome is still in its infancy, and there are some limitations to the American Gut project.

First, it’s a research project and cannot provide diet or lifestyle advice. And, for the most part it’s too early to use this sort of data to make dietary or clinical recommendations.

Exceptions to that include recommendations around improving gut diversity, where it’s well recognized from many studies that increasing the variety of plant foods in your diet improves diversity. Hopefully with more data and research in the future, we’ll be able to make more tailored guidance based on one’s microbiome.

Second – and related to the first point – the findings from the American Gut project so far are simply static observations; research on longitudinal data (data over time) or clinical trials is lacking. In many cases, we cannot extrapolate whether a certain aspect of the gut microbiome has a definite effect on health.

One goal of the American Gut project is for it to be an open resource for human microbiome data. Anyone can participate (for $99) and data is anonymized so that any person who’s interested can – for free – download their data or the data of everyone who’s contributed to the project thus far. This open resource will hopefully accelerate microbiome research since access to the data is public.

Further reading