mSystems (Jun 2018)
American Gut: an Open Platform for Citizen Science Microbiome Research
- 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,
- 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 Vázquez-Baeza,
- Alison Vrbanac,
- Paul Wischmeyer,
- Elaine Wolfe,
- Qiyun Zhu,
- Rob Knight
Affiliations
- Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Embriette Hyde
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Justine W. Debelius
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- James T. Morton
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Alexander A. Aksenov
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA
- Bahar Behsaz
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Caitriona Brennan
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Yingfeng Chen
- Department of Biology, San Diego State University, San Diego, California, USA
- Lindsay DeRight Goldasich
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA
- Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
- Ashkaan K. Fahimipour
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA
- James Gaffney
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Jack A. Gilbert
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
- Grant Gogul
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Jessica L. Green
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA
- Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, QLD, Australia
- Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Curtis Huttenhower
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Matthew A. Jackson
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
- Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Dilip V. Jeste
- Departments of Psychiatry and Neurosciences, University of California San Diego, La Jolla, California, USA
- Lingjing Jiang
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, California, USA
- Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
- Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Joshua Ladau
- The Gladstone Institutes, University of California, San Francisco, California, USA
- Jeff Leach
- Human Food Project, Terlingua, Texas, USA
- Clarisse Marotz
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Dmitry Meleshko
- St. Petersburg State University, Center for Algorithmic Biotechnology, Saint Petersburg, Russia
- Alexey V. Melnik
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA
- Jessica L. Metcalf
- Department of Animal Science, Colorado State University, Fort Collins, Colorado, USA
- Hosein Mohimani
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
- Emmanuel Montassier
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
- Jose Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Tanya T. Nguyen
- Departments of Psychiatry and Neurosciences, University of California San Diego, La Jolla, California, USA
- Shyamal Peddada
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pavel Pevzner
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA
- Katherine S. Pollard
- The Gladstone Institutes, University of California, San Francisco, California, USA
- Gholamali Rahnavard
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Adam Robbins-Pianka
- Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, USA
- Naseer Sangwan
- Department of Biosciences, Argonne National Laboratory, Chicago, Illinois, USA
- Joshua Shorenstein
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Larry Smarr
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Timothy Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, United Kingdom
- Austin D. Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Varykina G. Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Luke R. Thompson
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA
- Anupriya Tripathi
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Alison Vrbanac
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Paul Wischmeyer
- Department of Anesthesiology and Surgery, Duke University School of Medicine, Durham, North Carolina, USA
- Elaine Wolfe
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- DOI
- https://doi.org/10.1128/mSystems.00031-18
- Journal volume & issue
-
Vol. 3,
no. 3
Abstract
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.
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