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.; Mann, Allison E.; Amir, Amnon; Frazier, Angel; Martino, Cameron; Lebrilla, Carlito; Lozupone, Catherine; Lewis, Cecil M.; Raison, Charles; Zhang, Chi; Lauber, Christian L.; Warinner, Christina; Lowry, Christopher A.; Callewaert, Chris; Bloss, Cinnamon; Willner, Dana; Galzerani, Daniela Domingos; Gonzalez, David J.; Mills, David A.; Chopra, Deepak; Gevers, Dirk; Berg-Lyons, Donna; Sears, Dorothy D.; Wendel, Doug; Lovelace, Elijah; Pierce, Emily; TerAvest, Emily; Bolyen, Evan; Bushman, Frederic D.; Wu, Gary D.; Church, George M.; Saxe, Gordon; Holscher, Hanna D.; Ugrina, Ivo; German, J. Bruce; Caporaso, J. Gregory; Wozniak, Jacob M.; Kerr, Jacqueline; Ravel, Jacques; Lewis, James D.; Suchodolski, Jan S.; Jansson, Janet K.; Hampton-Marcell, Jarrad T.; Bobe, Jason; Raes, Jeroen; Chase, John H.; Eisen, Jonathan A.; Monk, Jonathan; Clemente, Jose C.; Petrosino, Joseph; Goodrich, Julia; Gauglitz, Julia; Jacobs, Julian; Zengler, Karsten; Swanson, Kelly S.; Lewis, Kim; Mayer, Kris; Bittinger, Kyle; Dillon, Lindsay; Zaramela, Livia S.; Schriml, Lynn M.; Dominguez-Bello, Maria G.; Jankowska, Marta M.; Blaser, Martin; Pirrung, Meg; Minson, Michael; Kurisu, Mike; Ajami, Nadim; Gottel, Neil R.; Chia, Nicholas; Fierer, Noah; White, Owen; Cani, Patrice D.; Gajer, Pawel; Strandwitz, Philip; Kashyap, Purna; Dutton, Rachel; Park, Rachel S.; Xavier, Ramnik J.; Mills, Robert H.; Krajmalnik-Brown, Rosa; Ley, Ruth; Owens, Sarah M.; Klemmer, Scott; Matamoros, Sébastien; Mirarab, Siavash; Moorman, Stephanie; Holmes, Susan; Schwartz, Tara; Eshoo-Anton, Tifani W.; Vigers, Tim; Pandey, Vineet; Treuren, Will Van; Fang, Xin; Zech Xu, Zhenjiang; Jarmusch, Alan; Geier, Justin; Reeve, Nicolai; Silva, Ricardo; Kopylova, Evguenia; Nguyen, Dominic; Sanders, Karenina; Salido Benitez, Rodolfo Antonio; Heale, Arthur Cole; Abramson, Max; Waldispühl, Jérôme; Butyaev, Alexander; Drogaris, Chris; Nazarova, Elena; Ball, Madeleine; Gunderson, Beau

doi:10.1128/mSystems.00031-18

American Gut: an Open Platform for Citizen Science Microbiome Research

Journal Article · Tue May 15 00:00:00 EDT 2018 · mSystems

DOI:https://doi.org/10.1128/mSystems.00031-18· OSTI ID:1493907

; 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 more »

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 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.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDOE Office of Science (SC)

Contributing Organization:: American Gut Project (AGP)

Grant/Contract Number:: AC02-06CH11357; AC05-76RL01830

OSTI ID:: 1493907

Alternate ID(s):: OSTI ID: 1504427

Report Number(s):: PNNL-SA--113423; 148306

Journal Information:: mSystems, Journal Name: mSystems Journal Issue: 3 Vol. 3; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Temporal variability is a personalized feature of the human microbiome Flores, Gilberto E.; Caporaso, J. Gregory; Henley, Jessica B. Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0531-y	journal	December 2014
Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection Weingarden, Alexa; González, Antonio; Vázquez-Baeza, Yoshiki Microbiome, Vol. 3, Issue 1 https://doi.org/10.1186/s40168-015-0070-0	journal	March 2015
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Physiological and microbial adjustments to diet quality permit facultative herbivory in an omnivorous lizard Kohl, Kevin D.; Brun, Antonio; Magallanes, Melisa The Journal of Experimental Biology, Vol. 219, Issue 12 https://doi.org/10.1242/jeb.138370	journal	June 2016
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Fitting Linear Mixed-Effects Models Using lme4 Douglas, Bates,; Martin, Mächler,; Ben, Bolker, ETH Zurich https://doi.org/10.3929/ethz-b-000105397	text	January 2015
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A communal catalogue reveals Earth's multiscale microbial diversity Thompson, Luke; Sanders, Jon; McDonald, Daniel Zenodo, 33 files (CSV, TSV, BIOM, TXT, GZ, RDB); 47.3 GB https://doi.org/10.5281/zenodo.889999	dataset	November 2017
movie_s1.mp4 McDonald, Daniel; Robbins-Pianka, Adam; Mann, Allison E. figshare-American Gut Project, 1 MP4 file (11.64 MB) https://doi.org/10.6084/m9.figshare.5936479	media	February 2018
movie_s2.mp4 McDonald, Daniel; Robbins-Pianka, Adam; Mann, Allison E. figshare-American Gut Project, 1 MP4 file (7.04 MB) https://doi.org/10.6084/m9.figshare.5936482	media	February 2018
Unweighted UniFrac distances McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam Figshare https://doi.org/10.6084/m9.figshare.6131024	dataset	January 2018
Unweighted UniFrac distances McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam figshare https://doi.org/10.6084/m9.figshare.6131024.v1	dataset	January 2018
Weighted normalized UniFrac distances McDonald, Daniel; Robbins-Pianka, Adam; Mann, Allison E. figshare, 1 TXT.GZ file (730.39 MB) https://doi.org/10.6084/m9.figshare.6133121	dataset	April 2018
American Gut Project fecal sOTU counts table McDonald, Daniel; Robbins-Pianka, Adam; Mann, Allison E. figshare, 1 BIOM file (23.92 MB) https://doi.org/10.6084/m9.figshare.6137192	dataset	April 2018
American Gut Project fecal sOTU counts table McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam figshare https://doi.org/10.6084/m9.figshare.6137192.v1	dataset	January 2018
American Gut Project fecal sOTU relative abundance table McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam Figshare https://doi.org/10.6084/m9.figshare.6137198	dataset	January 2018
American Gut Project fecal sOTU relative abundance table McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam figshare https://doi.org/10.6084/m9.figshare.6137198.v1	dataset	January 2018
ag_tree.tre McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam Figshare https://doi.org/10.6084/m9.figshare.6137270	dataset	January 2018
American Gut collated alpha diversities McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam Figshare https://doi.org/10.6084/m9.figshare.6137312	dataset	January 2018
American Gut collated alpha diversities McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam figshare https://doi.org/10.6084/m9.figshare.6137312.v1	dataset	January 2018
Full American Gut Project mapping file McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam Figshare https://doi.org/10.6084/m9.figshare.6137315	dataset	January 2018
Full American Gut Project mapping file McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam figshare https://doi.org/10.6084/m9.figshare.6137315.v1	dataset	January 2018
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Bracken: estimating species abundance in metagenomics data Lu, Jennifer; Breitwieser, Florian P.; Thielen, Peter PeerJ Computer Science, Vol. 3 https://doi.org/10.7717/peerj-cs.104	journal	January 2017
Atropos: specific, sensitive, and speedy trimming of sequencing reads Didion, John P.; Martin, Marcel; Collins, Francis S. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3720	journal	January 2017

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