King's College London

Research portal

American Gut: an Open Platform for Citizen Science Microbiome Research

Research output: Contribution to journalArticle

Daniel McDonald, Embriette Hyde, Justine W Debelius, James T Morton, Antonio Gonzalez, Gail Ackermann, Alexander A Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C Dorrestein, Robert R Dunn, Ashkaan K Fahimipour, James Gaffney, Jack A Gilbert, Grant Gogul, Jessica L Green, Philip Hugenholtz, Greg Humphrey & 39 more Curtis Huttenhower, Matthew A Jackson, Stefan Janssen, Dilip V Jeste, Lingjing Jiang, Scott T Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V Melnik, Jessica L Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D Swafford, Varykina G Thackray, Luke R. Thompson, Anupriya Tripathi, Yoshiki Vazquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, American Gut Consortium , Rob Knight

Original languageEnglish
JournalmSystems
Volume3
Issue number3
DOIs
Publication statusPublished - 26 May 2018

King's Authors

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.

View graph of relations

© 2018 King's College London | Strand | London WC2R 2LS | England | United Kingdom | Tel +44 (0)20 7836 5454