Dataset Information

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

ABSTRACT: 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. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.

SUBMITTER: McDonald D

PROVIDER: S-EPMC5954204 | biostudies-literature | 2018 May-Jun

REPOSITORIES: biostudies-literature

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

McDonald Daniel D Hyde Embriette E Debelius Justine W JW Morton James T JT Gonzalez Antonio A Ackermann Gail G Aksenov Alexander A AA Behsaz Bahar B Brennan Caitriona C Chen Yingfeng Y DeRight Goldasich Lindsay L Dorrestein Pieter C PC Dunn Robert R RR Fahimipour Ashkaan K AK Gaffney James J Gilbert Jack A JA Gogul Grant G Green Jessica L JL Hugenholtz Philip P Humphrey Greg G Huttenhower Curtis C Jackson Matthew A MA Janssen Stefan S Jeste Dilip V DV Jiang Lingjing L Kelley Scott T ST Knights Dan D Kosciolek Tomasz T Ladau Joshua J Leach Jeff J Marotz Clarisse C Meleshko Dmitry D Melnik Alexey V AV Metcalf Jessica L JL Mohimani Hosein H Montassier Emmanuel E Navas-Molina Jose J Nguyen Tanya T TT Peddada Shyamal S Pevzner Pavel P Pollard Katherine S KS Rahnavard Gholamali G Robbins-Pianka Adam A Sangwan Naseer N Shorenstein Joshua J Smarr Larry L Song Se Jin SJ Spector Timothy T Swafford Austin D AD Thackray Varykina G VG Thompson Luke R LR Tripathi Anupriya A Vázquez-Baeza Yoshiki Y Vrbanac Alison A Wischmeyer Paul P Wolfe Elaine E Zhu Qiyun Q Knight Rob R

mSystems 20180515 3

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. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, ...[more]

PMID: 29795809

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Dataset Information

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

Publications

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

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