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American Gut: an Open Platform for Citizen Science Microbiome Research

McDonald, Daniel ; Hyde, Embriette ; Debelius, Justine W ; Morton, James T ; Gonzalez, Antonio ; Ackermann, Gail ; Aksenov, Alexander A ; Behsaz, Bahar ; Brennan, Caitriona ; Chen, Yingfeng ; DeRight Goldasich, Lindsay ; Dorrestein, Pieter C ; Dunn, Robert R ; Fahimipour, Ashkaan K ; Gaffney, James ; Gilbert, Jack A ; Gogul, Grant ; Green, Jessica L ; Hugenholtz, Philip ; Humphrey, Greg ; Huttenhower, Curtis ; Jackson, Matthew A ; Janssen, Stefan ; Jeste, Dilip V ; Jiang, Lingjing ; Kelley, Scott T ; Knights, Dan ; Kosciolek, Tomasz ; 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 ; Rahnavard, Gholamali ; Robbins-Pianka, Adam ; Sangwan, Naseer ; Shorenstein, Joshua ; Smarr, Larry ; Song, Se Jin ; Spector, Timothy ; Swafford, Austin D ; Thackray, Varykina G ; Thompson, Luke R ; Tripathi, Anupriya ; Vázquez-Baeza, Yoshiki ; Vrbanac, Alison ; Wischmeyer, Paul ; Wolfe, Elaine ; Zhu, Qiyun ; Knight, Rob Greene, Casey S.

mSystems, 2018-05, Vol.3 (3) [Periódico revisado por pares]

United States: American Society for Microbiology

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Título:
American Gut: an Open Platform for Citizen Science Microbiome Research
Autor: McDonald, Daniel ; Hyde, Embriette ; Debelius, Justine W ; Morton, James T ; Gonzalez, Antonio ; Ackermann, Gail ; Aksenov, Alexander A ; Behsaz, Bahar ; Brennan, Caitriona ; Chen, Yingfeng ; DeRight Goldasich, Lindsay ; Dorrestein, Pieter C ; Dunn, Robert R ; Fahimipour, Ashkaan K ; Gaffney, James ; Gilbert, Jack A ; Gogul, Grant ; Green, Jessica L ; Hugenholtz, Philip ; Humphrey, Greg ; Huttenhower, Curtis ; Jackson, Matthew A ; Janssen, Stefan ; Jeste, Dilip V ; Jiang, Lingjing ; Kelley, Scott T ; Knights, Dan ; Kosciolek, Tomasz ; 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 ; Rahnavard, Gholamali ; Robbins-Pianka, Adam ; Sangwan, Naseer ; Shorenstein, Joshua ; Smarr, Larry ; Song, Se Jin ; Spector, Timothy ; Swafford, Austin D ; Thackray, Varykina G ; Thompson, Luke R ; Tripathi, Anupriya ; Vázquez-Baeza, Yoshiki ; Vrbanac, Alison ; Wischmeyer, Paul ; Wolfe, Elaine ; Zhu, Qiyun ; Knight, Rob
Greene, Casey S.
Assuntos: BASIC BIOLOGICAL SCIENCES ; citizen science ; microbiome
É parte de: mSystems, 2018-05, Vol.3 (3)
Notas: USDOE Office of Science (SC)
National Science Foundation (NSF)
AC02-06CH11357; AC05-76RL01830
PNNL-SA-113423
Citation McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, The American Gut Consortium, Knight R. 2018. American Gut: an open platform for citizen science microbiome research. mSystems 3:e00031-18. https://doi.org/10.1128/mSystems.00031-18.
D. McDonald and E. Hyde contributed equally to this work.
Descrição: 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. 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 = 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.
Editor: United States: American Society for Microbiology
Idioma: Inglês

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American Gut: an Open Platform for Citizen Science Microbiome Research

United States: American Society for Microbiology

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