TY - JOUR

T1 - American Gut

T2 - an Open Platform for Citizen Science Microbiome Research

AU - Amer Gut Consortium

AU - McDonald, Daniel

AU - Hyde, Embriette

AU - Debelius, Justine W.

AU - Morton, James T.

AU - Gonzalez, Antonio

AU - Ackermann, Gail

AU - Aksenov, Alexander A.

AU - Behsaz, Bahar

AU - Brennan, Caitriona

AU - Chen, Yingfeng

AU - Goldasich, Lindsay DeRight

AU - Dorrestein, Pieter C.

AU - Dunn, Robert R.

AU - Fahimipour, Ashkaan K.

AU - Gaffney, James

AU - Gilbert, Jack A.

AU - Gogu, Grant

AU - Green, Jessica L.

AU - Hugenholtz, Philip

AU - Humphrey, Greg

AU - Huttenhower, Curtis

AU - Jackson, Matthew A.

AU - Janssen, Stefan

AU - Jeste, Dilip V.

AU - Jiang, Lingjing

AU - Kelley, Scott T.

AU - Knights, Dan

AU - Kosciolek, Tomasz

AU - Ladau, Joshua

AU - Leach, Jeff

AU - Marotz, Clarisse

AU - Meleshko, Dmitry

AU - Melnik, Alexey V.

AU - Metcalf, Jessica L.

AU - Mohimani, Hosein

AU - Montassier, Emmanuel

AU - Navas-Molina, Jose

AU - Nguyen, Tanya T.

AU - Peddada, Shyamal

AU - Pevzner, Pavel

AU - Pollard, Katherine S.

AU - Rahnavard, Gholamali

AU - Robbins-Pianka, Adam

AU - Sangwan, Naseer

AU - Shorenstein, Joshua

AU - Smarr, Larry

AU - Song, Se Jin

AU - Spector, Timothy

AU - Swafford, Austin D.

AU - Thackray, Varykina G.

PY - 2018

Y1 - 2018

N2 - 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.

AB - 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.

KW - citizen science

KW - microbiome

KW - CARBOHYDRATE-ACTIVE ENZYMES

KW - MAJOR DEPRESSIVE DISORDER

KW - MASS-SPECTROMETRY DATA

KW - MOLECULAR NETWORKING

KW - DIVERSITY

KW - BACTERIA

KW - METAGENOMICS

KW - COMMUNITIES

KW - DISCOVERY

KW - REGRESSION

UR - http://msystems.asm.org/lookup/doi/10.1128/mSystems.00031-18

UR - http://www.mendeley.com/research/american-gut-open-platform-citizen-science-microbiome-research

U2 - 10.1128/mSystems.00031-18

DO - 10.1128/mSystems.00031-18

M3 - статья

VL - 3

JO - Living Reviews in Solar Physics

JF - Living Reviews in Solar Physics

SN - 2367-3648

IS - 3

M1 - ARTN e00031-18

ER -