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American Gut: An Open Platform For Citizen Science Microbiome Research
Authors
Gail Ackermann
Alexander A. Aksenov
+31 more
Bahar Behsaz
Caitriona Brennan
Yingfeng Chen
Justine W. Debelius
Pieter C. Dorrestein
Robert R. Dunn
Ashkaan K. Fahimipour
James Gaffney
Jack A. Gilbert
Grant Gogul
Lindsay De Right Goldasich
Antonio Gonzalez
Jessica L. Green
Philip Hugenholtz
Greg Humphrey
Curtis Huttenhower
Embriette Hyde
Matthew A. Jackson
Stefan Janssen
Dilip V. Jeste
Lingjing Jiang
Scott T. Kelley
Rob Knight
Dan Knights
Daniel McDonald
James T. Morton
Alison Vrbanac
Yoshiki Vázquez-Baeza
Paul Wischmeyer
Elaine Wolfe
Qiyun Zhu
Publication date
1 June 2018
Publisher
The Aquila Digital Community
Abstract
Copyright © 2018 McDonald et al. 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
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Last time updated on 18/02/2021