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American Gut: an Open Platform for Citizen-Science Microbiome Research
Open accessPreprint — published as 10.1128/msystems.00031-18 · Paper page
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 USA, UK, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes as 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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“These participants also complete surveys about general health status, disease history, lifestyle data and food frequency.”
From Multimodal biomedical AI (2022) · cites this paper as [94]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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“The data featured in this article come from a set of 953,000 rRNA fragments sequenced from stool samples submitted by participants in the AGP25, powered by TMI (https://microsetta.ucsd.edu/).”
From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [25]
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“As another example, the American Gut Project collects microbiome data from self-selected participants across several countries 94 .”
From Multimodal biomedical AI (2022) · cites this paper as [94]
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“BLS is designed to improve a reference multiple alignment of 1 million 16S ribosomal RNA (rRNA) sequences from The Microsetta Initiative’s (TMI) American Gut Project (AGP)25, a citizen science initiative collecting gut microbial genomic data.”
From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [25]
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“We observed that BLS outperforms SEPP on many variables, including several that have been linked to gut microbe diversity and human health25,39–42.”
From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [25]
In the citing paper
“The human gut microbiome is itself shaped by a wide variety of environmental exposures, including diet (8, 9) and medication use (10–13)”
From Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response (2021) · cites this paper as [9]
In the citing paper
“A diverse diet, and in particular, the number of different types of plant foods consumed [35,78], has been associated with greater microbial alpha-diversity thought to provide an increased variety of substrates for numerous taxa proliferation [78,84].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [78]
In the citing paper
“Species Facealibacterium prausnitzii and genus Oscillospira, typically known to be SCFA fermenters, were increased in individuals who consumed more than 30 plant types a week in comparison to those who consumed less than 10 plant types [78].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [78]
In the citing paper
“The American Gut Project, a large citizen science open platform study, collected self-report dietary data (FFQs) and faecal samples amongst other measures from over 10,000 individuals, predominantly UK, USA, and Australian residents, confirmed these observations.”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [78]
In the citing paper
“Consistent with this hypothesis are reported findings from the American Gut Project showing that individuals who reported a mental disorder such as depression, schizophrenia, post-traumatic stress disorder (PTSD) or bipolar disorder had more in common with other people with mental disorders, in terms of the bacteria makeup of their gut microbiomes, than they did with their mentally healthy pairs.”
From Role of diet and its effects on the gut microbiome in the pathophysiology of mental disorders (2022) · cites this paper as [133]
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Self-citation
Metadata
- Authors
- McDonalda, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., Goldasich, L. D., Dorrestein, P. C., Dunn, R. R., Fahimipour, A. K., Gaffney, J., Gilbert, J. A., Gogul, G., Green, J. L., Hugenholtz, P., Humphrey, G., Huttenhower, C., Jackson, M. A., Janssen, S., Jeste, D. V., Jiang, L., Kelley, S. T., Knights, D., Kosciolek, T., Ladau, J., Leach, J., Marotz, C., Meleshko, D., Melnik, A. V., Metcalf, J. L., Mohimani, H., Montassier, E., Navas-Molina, J., Nguyen, T. T., Peddada, S., Pevzner, P., Pollard, K. S., Rahnavard, G., Robbins-Pianka, A., Sangwan, N., Shorenstein, J., Smarr, L., Song, S. J., Spector, T., Swafford, A. D., Thackray, V. G., Thompson, L. R., Tripathi, A., Vazquez-Baeza, Y., Vrbanac, A., Wischmeyer, P., Wolfe, E., Zhu, Q., The American Gut Consortium, & Knight, R.
- Affiliations
- University of California San Diego (US)
- San Diego State University (US)
- North Carolina State University (US)
- University of Oregon (US)
- Argonne National Laboratory (US)
- The University of Queensland (AU)
- Broad Institute (US)
- King's College London (GB)
- University of Minnesota (US)
- Gladstone Institutes (US)
- St Petersburg University (RU)
- Colorado State University (US)
- Carnegie Mellon University (US)
- University of Pittsburgh (US)
- National Oceanic and Atmospheric Administration (US)
- Duke University (US)
- Corresponding author
- Knight, Rob
- ORCID
- McDonalda, Daniel
- Debelius, Justine W.
- Morton, James T.
- Ackermann, Gail
- Aksenov, Alexander A.
- Brennan, Caitriona
- Chen, Yingfeng
- Goldasich, Lindsay DeRight
- Dorrestein, Pieter C.
- Dunn, Robert R.
- Fahimipour, Ashkaan K.
- Gaffney, James
- Gilbert, Jack A
- Gogul, Grant
- Hugenholtz, Philip
- Huttenhower, Curtis
- Jackson, Matthew A.
- Janssen, Stefan
- Jeste, Dilip V.
- Jiang, Lingjing
- Kelley, Scott T.
- Knights, Dan
- Ladau, Joshua
- Leach, Jeff
- Marotz, Clarisse
- Meleshko, Dmitry
- Melnik, Alexey V.
- Metcalf, Jessica L.
- Mohimani, Hosein
- Montassier, Emmanuel
- Navas-Molina, Jose
- Nguyen, Tanya T.
- Peddada, Shyamal
- Pevzner, Pavel
- Pollard, Katherine S.
- Sangwan, Naseer
- Shorenstein, Joshua
- Smarr, Larry
- Song, Se Jin
- Swafford, Austin D.
- Thackray, Varykina G.
- Thompson, Luke R.
- Tripathi, Anupriya
- Vrbanac, Alison
- Wischmeyer, Paul
- Wolfe, Elaine
- Zhu, Qiyun
- Knight, Rob
- Venue
- mSystems
- Publisher
- openRxiv
- Published
- 2018-03-07
- Volume
- 3
- Issue
- 3
- ISSN
- 2379-5077 (ISSN-L)
- PMC
- PMC5954204
- OpenAlex
- W2794407684
- Cited by
- 878
- References
- 121
- Citations by year
- 2026: 59 · 2025: 114 · 2024: 106 · 2023: 100 · 2022: 137 · 2021: 132 · 2020: 108 · 2019: 90 · 2018: 30
- FWCI
- 32.11
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- mSystems (publishedVersion, public-domain)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Ghent University Academic Bibliography (Ghent University) (publishedVersion, other-oa)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion, public-domain)
- NOAA Institutional Repository (submittedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, public-domain)
- Digital Access to Libraries (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Research Portal (King's College London) (submittedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- PUB – Publications at Bielefeld University (Bielefeld University) (submittedVersion)
- Publikationen an der Universität Bielefeld (Universität Bielefeld) (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- National Science Foundation (1144807, DE-AC02–06CH11357, 1053575)
- U.S. Department of Energy (DE‐ AC02‐06CH11357, ACI-1053575, AC02‐06CH11357, 06CH11357, DE-AC02-)
- Alfred P. Sloan Foundation
- Wellcome Trust
- San Diego Supercomputer Center
- National Institute for Health and Care Research (NF-SI-0507-10228, NF-SI-0514-10027)
- King's College London
- Russian Science Foundation (14‐50‐00069, 14-50-)
- Société Nationale Française de Gastro-Entérologie
- Walloon excellence in life sciences and biotechnology
- University of Colorado Boulder (DE-AC02-06CH11357)
- University of California, San Diego (DE-AC02-06CH11357)
- Hansjörg Wyss Institute for Biologically Inspired Engineering, Harvard University
- Medical Research Council (MR/N030125/1, MR/N01183X/1)
- National Institute of General Medical Sciences (T32GM007752)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK042086, P30DK043351)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- citizen science, microbiome research, untargeted metabolomics, gut microbiota
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