Image: The HiSeq 2500 system is a powerful high-throughput sequencing system (Photo courtesy of Illumina).
Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown.
Two projects have been launched, the American Gut Project (AGP) in November 2012 as a collaboration between the Earth Microbiome Project (EMP) and the Human Food Project (HFP) to discover the kinds of microbes and microbiomes “in the wild” via a self-selected citizen-scientist cohort.
A large team of international scientists collaborating with the University of California, San Diego (La Jolla, CA, USA) received stool samples from individuals in the USA, 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.
The team used MiSeq or HiSeq instruments to sequence 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. The team was 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.
When it came to diet, the scientists 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.
Daniel McDonald, PhD, a scientific director for American Gut and the lead author of the study, said, “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.” The study was published on May 15, 2018, in the journal mSystems.
University of California, San Diego