American Gut: an Open Platform for Citizen Science Microbiome Research
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...
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American Society for Microbiology
2018
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oai:doaj.org-article:0301cbad620f4f3490bc93e225ec5d0c2021-12-02T18:15:45ZAmerican Gut: an Open Platform for Citizen Science Microbiome Research10.1128/mSystems.00031-182379-5077https://doaj.org/article/0301cbad620f4f3490bc93e225ec5d0c2018-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00031-18https://doaj.org/toc/2379-5077ABSTRACT 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.Daniel McDonaldEmbriette HydeJustine W. DebeliusJames T. MortonAntonio GonzalezGail AckermannAlexander A. AksenovBahar BehsazCaitriona BrennanYingfeng ChenLindsay DeRight GoldasichPieter C. DorresteinRobert R. DunnAshkaan K. FahimipourJames GaffneyJack A. GilbertGrant GogulJessica L. GreenPhilip HugenholtzGreg HumphreyCurtis HuttenhowerMatthew A. JacksonStefan JanssenDilip V. JesteLingjing JiangScott T. KelleyDan KnightsTomasz KosciolekJoshua LadauJeff LeachClarisse MarotzDmitry MeleshkoAlexey V. MelnikJessica L. MetcalfHosein MohimaniEmmanuel MontassierJose Navas-MolinaTanya T. NguyenShyamal PeddadaPavel PevznerKatherine S. PollardGholamali RahnavardAdam Robbins-PiankaNaseer SangwanJoshua ShorensteinLarry SmarrSe Jin SongTimothy SpectorAustin D. SwaffordVarykina G. ThackrayLuke R. ThompsonAnupriya TripathiYoshiki Vázquez-BaezaAlison VrbanacPaul WischmeyerElaine WolfeQiyun ZhuRob KnightAmerican Society for Microbiologyarticlecitizen sciencemicrobiomeMicrobiologyQR1-502ENmSystems, Vol 3, Iss 3 (2018) |
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DOAJ |
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DOAJ |
| language |
EN |
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citizen science microbiome Microbiology QR1-502 |
| spellingShingle |
citizen science microbiome Microbiology QR1-502 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 American Gut: an Open Platform for Citizen Science Microbiome Research |
| description |
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. |
| format |
article |
| author |
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 |
| author_facet |
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 |
| author_sort |
Daniel McDonald |
| title |
American Gut: an Open Platform for Citizen Science Microbiome Research |
| title_short |
American Gut: an Open Platform for Citizen Science Microbiome Research |
| title_full |
American Gut: an Open Platform for Citizen Science Microbiome Research |
| title_fullStr |
American Gut: an Open Platform for Citizen Science Microbiome Research |
| title_full_unstemmed |
American Gut: an Open Platform for Citizen Science Microbiome Research |
| title_sort |
american gut: an open platform for citizen science microbiome research |
| publisher |
American Society for Microbiology |
| publishDate |
2018 |
| url |
https://doaj.org/article/0301cbad620f4f3490bc93e225ec5d0c |
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