American Gut: An open platform for citizen science microbiome research

American Gut Consortium

Research output: Contribution to journalArticlepeer-review

120 Scopus citations

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.

Original languageEnglish (US)
Article numbere00031-18
JournalmSystems
Volume3
Issue number3
DOIs
StatePublished - Jun 2018

Bibliographical note

Funding Information:
We thank first all the citizen science volunteers around the world. We also thank Katherine Amato, Margaret K. Butler, Gabriela Surdulescu, Luke Ursell, Jeff DeReus, Evguenia Kopylova, John Graham, Victoria Vazquez, Jai Ram Rideout, Merete Eggesbo, Steve Green, Kathy Holt, Jim Huntley, Zehra Esra Ilhan, Daniel Mayer, Catherine Nicholas, Laura Parfrey, Juanma Peralta, Dorota Porazinska, Jennifer Smilowitz, Matt Gebert, Se Jin Song, Kumar Thurimella, Sam Way, Tony Walters, Sophie Weiss, Ulla Westermann, Shawnelle White, Doug Woodhams, Jerry Kennedy, Scott Handley, Chandni Desai, Carolina Carpenter, Gabriella Fanelli, Deborah L. Bright, and Xochitl C. Morgan for their contributions to the American Gut Project. Some sequencing was conducted by Mahdieh Khosroheidari and Clifford L. Green at the IGM Genomics Center, University of California, San Diego, La Jolla, CA. We thank the BioFrontiers Institute for their administrative support for the project while it was based at the University of Colorado Boulder. Crowdfunding support was provided through Indiegogo and FundRazr. Some consortium members were supported by NSF IGERT award 1144807, the Sloan Foundation Microbiology of the Built Environment Program, the Wyss Institute, the Howard Hughes Medical Institute, the U.S. Department of Energy under contract DE-AC02-06CH11357.NS, the ERC Starting Grant 2013 (European Research Council, starting grant 336452-ENIGMO), WELBIO WELBIO-CR-2012S-02R, and the Robert Tour-nut award (Soci?t? Nationale Fran?aise de Gastro-Ent?rologie). The British Gut collection was carried out by the Department of Twin Research at KCL funded by the Wellcome Trust, MRC, a JPI Dynamic grant, and the National Institute for Health Research (NIHR) Clinical Research Facility at Guy?s & St Thomas? NHS Foundation Trust and NIHR Biomedical Research Centre based at Guy?s and St. Thomas? NHS Foundation Trust and King?s College London. Tim Spector is an NIHR Senior Investigator. Dmitry Meleshko was supported by Russian Science Foundation (grant number 14-50-00069). Parts of the computations were performed using the San Diego Supercomputer Center (SDSC) through XSEDE allocations, which are supported by the NSF grant ACI-1053575. All authors are members of the American Gut Consortium. The American Gut Consortium also includes the following persons: Allison E. Mann, Amnon Amir, Angel Frazier, Cameron Martino, Carlito Lebrilla, Catherine Lozupone, Cecil M. Lewis, Jr., Charles Raison, Chi Zhang, Christian L. Lauber, Christina Warinner, Christopher A. Lowry, Chris Callewaert, Cinnamon 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 Pierce, Emily TerAvest, Evan Bolyen, Frederic D. Bushman, Gary D. Wu, George M. Church, Gordon Saxe, Hannah D. Holscher, Ivo Ugrina, J. Bruce German, J. Gregory Caporaso, Jacob M. Wozniak, Jacqueline Kerr, Jacques Ravel, James D. Lewis, Jan S. Suchodolski, Janet K. Jansson, Jarrad T. Hampton-Marcell, Jason Bobe, Jeroen Raes, John H. Chase, Jonathan A. Eisen, Jonathan Monk, Jose C. Clemente, Joseph Petrosino, Julia Goodrich, Julia Gauglitz, Julian Jacobs, Karsten Zengler, Kelly S. Swanson, Kim Lewis, Kris Mayer, Kyle Bittinger, Lindsay Dillon, Livia S. Zaramela, Lynn M. Schriml, Maria G. Dominguez-Bello, Marta M. Jankowska, Martin Blaser, Meg Pirrung, Michael Minson, Mike Kurisu, Nadim Ajami, Neil R. Gottel, Nicholas Chia, Noah Fierer, Owen White, Patrice D. Cani, Pawel Gajer, Philip Strandwitz, Purna Kashyap, Rachel Dutton, Rachel S. Park, Ramnik J. Xavier, Robert H. Mills, Rosa Krajmalnik-Brown, Ruth Ley, Sarah M. Owens, Scott Klemmer, S?bastien 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 Jarmusch, Justin Geier, Nicolai Reeve, Ricardo Silva, Evguenia Kopylova, Dominic Nguyen, Karenina Sanders, Rodolfo Antonio Salido Benitez, Arthur Cole Heale, Max Abramson, J?r?me Waldisp?hl, Alexander Butyaev, Chris Drogaris, Elena Nazarova, Madeleine Ball, and Beau Gunderson.

Funding Information:
Crowdfunding support was provided through Indiegogo and FundRazr. Some consortium members were supported by NSF IGERT award 1144807, the Sloan Foundation Microbiology of the Built Environment Program, the Wyss Institute, the Howard Hughes Medical Institute, the U.S. Department of Energy under contract DE-AC02-06CH11357.NS, the ERC Starting Grant 2013 (European Research Council, starting grant 336452-ENIGMO), WELBIO WELBIO-CR-2012S-02R, and the Robert Tour-nut award (Société Nationale Française de Gastro-Entérologie). The British Gut collection was carried out by the Department of Twin Research at KCL funded by the Wellcome Trust, MRC, a JPI Dynamic grant, and the National Institute for Health Research (NIHR) Clinical Research Facility at Guy’s & St Thomas’ NHS Foundation Trust and NIHR Biomedical Research Centre based at Guy’s and St. Thomas’ NHS Foundation Trust and King’s College London. Tim Spector is an NIHR Senior Investigator. Dmitry Meleshko was supported by Russian Science Foundation (grant number 14-50-00069). Parts of the computations were performed using the San Diego Supercomputer Center (SDSC) through XSEDE allocations, which are supported by the NSF grant ACI-1053575.

Publisher Copyright:
Copyright © 2018 McDonald et al.

Keywords

  • Citizen science
  • Microbiome

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