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American Gut Project Reports Microbiome Results for 11K Participants

NEW YORK (GenomeWeb) – Members of the American Gut Consortium have shared microbiome findings from their citizen science project, which has enrolled more than 11,000 participants so far.

As they reported in the journal mSystems today, the researchers received stool samples from individuals in the US, UK, and dozens of other countries. Participants completed voluntary surveys related to their diet, lifestyle, health status, and disease history, including nearly 1,800 individuals who took part in a picture-based food frequency questionnaire.

With these data, the team has started parsing relationships between gut microbial composition, diet, psychiatric disease, and more. The results suggest that gut microbiome diversity ticks up in individuals who eat a greater variety of plants, for example, but wanes in those with recent antibiotic use. The collection is continuing to grow, and investigators hope to do more extensive and detailed analyses on the samples in the future.

"The American Gut Project is dynamic, with samples arriving from around the world daily," corresponding author Rob Knight, director of the University of California, San Diego's Center for Microbiome Innovation, said in a statement.

"The analysis presented in this paper represents a single snapshot," he explained, "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."

Researchers involved in two other large microbiome profiling projects — the Earth Microbiome Project (EMP) and the Human Food Project — came together to establish the American Gut Project. Since the effort kicked off in 2012, it has enrolled 11,336 individuals, received 15,096 samples, and profiled more than 9,500 fecal samples, using more than $2.5 million contributed to the American Gut Project and a related British Gut project through crowd funding sites.

Using Illumina MiSeq or HiSeq instruments, the investigators sequenced 16S rRNA V4 regions in the samples to characterize their microbial composition. They also cultured a subset of samples, which were subjected to shotgun metagenomic sequencing with the Illumina HiSeq 2500 and metabolite profiling by high-performance liquid chromatography and mass spectrometry (HPLC-MS).

In addition to pronounced overall microbial diversity, the team noted that differences found between one gut microbiome and the next were sometimes on par with those described in distinct environments for the EMP.

"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," first author Daniel McDonald, a scientific director for American Gut who is based at the UCSD School of Medicine, said in a statement.

Although the samples were shipped at room temperature through the mail, the team reported, they yielded microbiome composition patterns comparable to those reported previously, particularly after correcting for enhanced microbial growth during this process.

When it came to diet, the researchers detected ties between the number of plant types individuals consumed and their gut microbial diversity, regardless of whether their overall diet was vegan or vegetarian. Likewise, those who reported eating plant-rich fare (30 types of plants per week or more) were less apt to carry bugs with antibiotic resistance genes compared to those who consumed 10 types of plants per week or fewer.

Perhaps more unexpectedly, the team's comparison of 139 recent users of antibiotics and 117 individuals who were antibiotic-free for a year or more revealed rising metabolomic diversity following antibiotic use, despite falling microbial diversity,

The researchers were also able to profile gut microbiome composition in individuals with or without psychiatric conditions such as depression, schizophrenia, bipolar disorder, or post-traumatic stress disorder, uncovering gut microbiomes that clustered apart from those of 125 unaffected individuals.

Also, longitudinal samples from an individual undergoing large bowel resection offered a look at the gut microbiome dynamics at 58 time points before and after the surgery. 

Still other analyses are anticipated as the American Gut Project collection grows, the authors noted, explaining that the project's open community Research Network process "allows a 'living analysis' approach, embracing new researchers and analytical tools on an ongoing basis."