American Gut: an Open Platform for Citizen Science Microbiome Research.

Area of Science:

• Microbiology
• Human Health
• Citizen Science

Background:

• Integrating microbiome data from diverse projects is challenging.
• The full extent of microbial and molecular diversity in human stool is largely unknown.
• Standardized protocols are needed for robust microbiome research.

Purpose of the Study:

• To compare human stool microbiome specimens from a large citizen-science cohort.
• To investigate microbial and molecular diversity in the human gut.
• To explore associations between the microbiome, metabolome, and dietary plant diversity.

Main Methods:

• Utilized standardized protocols from the Earth Microbiome Project.
• Collected over 10,000 human stool samples from citizen-scientists.
• Employed an open research network for data integration and analysis.
• Applied untargeted metabolomics to hundreds of samples.

Main Results:

• Observed a wide range of beta-diversity in human stool microbiomes, exceeding environmental samples.
• Identified procedures to correct for room-temperature shipping overgrowth, enabling phenotype correlations.
• Discovered novel molecules and molecular communities within the human stool metabolome.
• Confirmed associations between the microbiome and psychiatric illness and documented microbiome changes during surgery.

Conclusions:

• Citizen science, using room-temperature shipped samples, can replicate and extend findings from clinical cohorts.
• Individual microbiome changes, such as post-surgery, can be more significant than environmental biome differences.
• Dietary plant diversity is a key factor influencing the human microbiome and metabolome.