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mSystems. 2018 May 15;3(3). pii: e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun.

American Gut: an Open Platform for Citizen Science Microbiome Research.

Author information

1
Department of Pediatrics, University of California San Diego, La Jolla, California, USA.
2
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA.
3
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA.
4
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA.
5
Department of Biology, San Diego State University, San Diego, California, USA.
6
Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA.
7
Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA.
8
Department of Surgery, University of Chicago, Chicago, Illinois, USA.
9
Institute for Genomic and Systems Biology, University of Chicago, Chicago, Illinois, USA.
10
Department of Biosciences, Argonne National Laboratory, Chicago, Illinois, USA.
11
Marine Biology Laboratory, University of Chicago, Chicago, Illinois, USA.
12
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, QLD, Australia.
13
Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA.
14
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
15
Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom.
16
Departments of Psychiatry and Neurosciences, University of California San Diego, La Jolla, California, USA.
17
Sam and Rose Stein Institute for Research on Aging and Center for Healthy Aging, University of California San Diego, La Jolla, California, USA.
18
Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA.
19
Biotechnology Institute, University of Minnesota, Minneapolis, Minnesota, USA.
20
The Gladstone Institutes, University of California, San Francisco, California, USA.
21
Human Food Project, Terlingua, Texas, USA.
22
St. Petersburg State University, Center for Algorithmic Biotechnology, Saint Petersburg, Russia.
23
Department of Animal Science, Colorado State University, Fort Collins, Colorado, USA.
24
Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
25
Université de Nantes, Microbiotas Hosts Antibiotics and Bacterial Resistances (MiHAR), Nantes, France.
26
Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
27
Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA.
28
Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, USA.
29
California Institute for Telecommunications and Information Technology (Calit2), University of California San Diego, La Jolla, California, USA.
30
Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA.
31
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.
32
Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA.
33
Department of Anesthesiology and Surgery, Duke University School of Medicine, Durham, North Carolina, USA.
34
Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA.
#
Contributed equally

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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