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American Gut: an Open Platform for Citizen Science Microbiome Research

2018; American Society for Microbiology; Volume: 3; Issue: 3 Linguagem: Inglês

10.1128/msystems.00031-18

2379-5077

Daniel McDonald, Embriette R. Hyde, Justine W. Debelius, James T. Morton, Antonio González-Torres, 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, Curtis Huttenhower, Matthew Jackson, Stefan Janssen, Dilip V. Jeste, Lingjing Jiang, Scott T. Kelley, Dan Knights, Tomasz Kościółek, Joshua Ladau, Jeff D. Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V. Melnik, Jessica L. Metcalf, Hosein Mohimani, Emmanuel Montassier, José A. Navas-Molina, Tanya T. Nguyen, Shyamal D. Peddada, Pavel A. Pevzner, Katherine S. Pollard, Ali Rahnavard, Adam Robbins‐Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D. Swafford, Varykina G. Thackray, Luke Thompson, Anupriya Tripathi, Yoshiki Vázquez‐Baeza, Alison Vrbanac, Paul E. Wischmeyer, Elaine Wolfe, Qiyun Zhu, Rob Knight, Allison E. Mann, Amnon Amir, Angel Frazier, Cameron Martino, Carlito B. Lebrilla, Catherine Lozupone, Cecil M. Lewis, Charles L. Raison, Chi Zhang, Christian L. Lauber, Christina Warinner, Christopher A. Lowry, Chris Callewaert, Cinnamon S. Bloss, Dana Willner, Daniela Domingos Galzerani, David J. Gonzalez, David A. Mills, Deepak Chopra, Dirk Gevers, Donna Berg-Lyons, Dorothy D. Sears, Doug Wendel, Elijah Lovelace, Emily C. Pierce, Emily TerAvest, Evan Bolyen, Frederic D. Bushman, Gary D. Wu, George M. Church, Gordon Saxe, Hanna D. Holscher, Ivo Ugrina, J German, J. Gregory Caporaso, Jacob M. Wozniak, Jacqueline Kerr, Jacques Ravel, James D. Lewis, Jan S. Suchodolski, Janet Jansson, Jarrad Hampton‐Marcell, Jason Bobe, Jeroen Raes, John Chase, Jonathan A. Eisen, Jonathan M. Monk, José C. Clemente, Joseph F. Petrosino, Julia K. Goodrich, Julia M. Gauglitz, Julian Jacobs, Karsten Zengler, Kelly S. Swanson, Kim Lewis, Kris Mayer, Kyle Bittinger, Lindsay Dillon, Lívia S. Zaramela, Lynn M. Schriml, Maria Gloria Dominguez‐Bello, Marta M. Jankowska, Martin J. Blaser, Meg Pirrung, Michael Minson, Mike Kurisu, Nadim J. Ajami, Neil Gottel, Nicholas Chia, Noah Fierer, Owen White, Patrice D. Cani, Pawel Gajer, Philip Strandwitz, Purna Kashyap, Rachel J. Dutton, Rachel S. Park, Ramnik J. Xavier, Robert H. Mills, Rosa Krajmalnik‐Brown, Ruth E. Ley, Sarah M. Owens, Scott Klemmer, Sébastien Matamoros, Siavash Mirarab, Stephanie Moorman, Susan Holmes, Tara Schwartz, Tifani W. Eshoo-Anton, Tim Vigers, Vineet Pandey, Will Van Treuren, Xin Fang, Zhenjiang Zech Xu, Alan K. Jarmusch, Justin Geier, Nicolai Reeve, Ricardo Silva, Evguenia Kopylova, Dominic Nguyen, Karenina Sanders, Rodolfo Antonio Salido Benítez, Arthur Cole Heale, Max Abramson, Jérôme Waldispühl, Alexander Butyaev, Chris Drogaris, Elena Nazarova, Mad Price Ball, Beau Gunderson,

Microbial Community Ecology and Physiology

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.