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

Title: 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 »

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. IMPORTANCEWe 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 integratingn= 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)

Cite

Export

Save

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, Vol. 3, Issue 3; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 404 works

Citation information provided by
Web of Science

References (122)

How gut microbes talk to organs: The role of endocrine and nervous routes Cani, Patrice D.; Knauf, Claude Molecular Metabolism, Vol. 5, Issue 9 https://doi.org/10.1016/j.molmet.2016.05.011	journal	September 2016
Balance Trees Reveal Microbial Niche Differentiation Morton, James T.; Sanders, Jon; Quinn, Robert A. mSystems, Vol. 2, Issue 1 https://doi.org/10.1128/mSystems.00162-16	journal	January 2017
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania Smits, Samuel A.; Leach, Jeff; Sonnenburg, Erica D. Science, Vol. 357, Issue 6353 https://doi.org/10.1126/science.aan4834	journal	August 2017
Strains, functions and dynamics in the expanded Human Microbiome Project Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali Nature, Vol. 550, Issue 7674 https://doi.org/10.1038/nature23889	journal	September 2017
Minireview: Gut Microbiota: The Neglected Endocrine Organ Clarke, Gerard; Stilling, Roman M.; Kennedy, Paul J. Molecular Endocrinology, Vol. 28, Issue 8 https://doi.org/10.1210/me.2014-1108	journal	August 2014
Marked seasonal variation in the wild mouse gut microbiota Maurice, Corinne F.; CL Knowles, Sarah; Ladau, Joshua The ISME Journal, Vol. 9, Issue 11 https://doi.org/10.1038/ismej.2015.53	journal	May 2015
A human gut microbial gene catalogue established by metagenomic sequencing Qin, Junjie; Li, Ruiqiang; Raes, Jeroen Nature, Vol. 464, Issue 7285 https://doi.org/10.1038/nature08821	journal	March 2010
Worlds within worlds: evolution of the vertebrate gut microbiota Ley, Ruth E.; Lozupone, Catherine A.; Hamady, Micah Nature Reviews Microbiology, Vol. 6, Issue 10 https://doi.org/10.1038/nrmicro1978	journal	October 2008
A new method for non-parametric multivariate analysis of variance: NON-PARAMETRIC MANOVA FOR ECOLOGY Anderson, Marti J. Austral Ecology, Vol. 26, Issue 1 https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x	journal	February 2001
Global marine bacterial diversity peaks at high latitudes in winter Ladau, Joshua; Sharpton, Thomas J.; Finucane, Mariel M. The ISME Journal, Vol. 7, Issue 9 https://doi.org/10.1038/ismej.2013.37	journal	March 2013
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy Wang, Q.; Garrity, G. M.; Tiedje, J. M. Applied and Environmental Microbiology, Vol. 73, Issue 16 https://doi.org/10.1128/AEM.00062-07	journal	June 2007
American Gut collated alpha diversities McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam Figshare https://doi.org/10.6084/m9.figshare.6137312	dataset	January 2018
Conjugated linoleic acid biosynthesis by human-derived Bifidobacterium species Coakley, M.; Ross, R. P.; Nordgren, M. Journal of Applied Microbiology, Vol. 94, Issue 1 https://doi.org/10.1046/j.1365-2672.2003.01814.x	journal	January 2003
Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides Nguyen, Don D.; Melnik, Alexey V.; Koyama, Nobuhiro Nature Microbiology, Vol. 2, Issue 1 https://doi.org/10.1038/nmicrobiol.2016.197	journal	October 2016
metaSPAdes: a new versatile metagenomic assembler Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.213959.116	journal	March 2017
UniFrac: an effective distance metric for microbial community comparison Lozupone, Catherine; Lladser, Manuel E.; Knights, Dan The ISME Journal, Vol. 5, Issue 2 https://doi.org/10.1038/ismej.2010.133	journal	September 2010
ag_tree.tre McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam Figshare https://doi.org/10.6084/m9.figshare.6137270	dataset	January 2018
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns Amir, Amnon; McDonald, Daniel; Navas-Molina, Jose A. mSystems, Vol. 2, Issue 2 https://doi.org/10.1128/mSystems.00191-16	journal	March 2017
Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees Liu, K.; Raghavan, S.; Nelesen, S. Science, Vol. 324, Issue 5934 https://doi.org/10.1126/science.1171243	journal	June 2009
Filtering for increased power for microarray data analysis Hackstadt, Amber J.; Hess, Ann M. BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-11	journal	January 2009
Fitting Linear Mixed-Effects Models Using lme4 Bates, Douglas; Mächler, Martin; Bolker, Ben Journal of Statistical Software, Vol. 67, Issue 1 https://doi.org/10.18637/jss.v067.i01	journal	January 2015
Kraken: ultrafast metagenomic sequence classification using exact alignments Wood, Derrick E.; Salzberg, Steven L. Genome Biology, Vol. 15, Issue 3 https://doi.org/10.1186/gb-2014-15-3-r46	journal	January 2014
Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping Amir, Amnon; McDonald, Daniel; Navas-Molina, Jose A. mSystems, Vol. 2, Issue 2 https://doi.org/10.1128/mSystems.00199-16	journal	March 2017
A communal catalogue reveals Earth’s multiscale microbial diversity Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel Nature, Vol. 551, Issue 7681 https://doi.org/10.1038/nature24621	journal	November 2017
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
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
Prokka: rapid prokaryotic genome annotation Seemann, T. Bioinformatics, Vol. 30, Issue 14 https://doi.org/10.1093/bioinformatics/btu153	journal	March 2014
Succession of microbial consortia in the developing infant gut microbiome Koenig, J. E.; Spor, A.; Scalfone, N. Proceedings of the National Academy of Sciences, Vol. 108, Issue Supplement_1 https://doi.org/10.1073/pnas.1000081107	journal	July 2010
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry Journal of Computational Biology, Vol. 19, Issue 5 https://doi.org/10.1089/cmb.2012.0021	journal	May 2012
Mass spectral molecular networking of living microbial colonies Watrous, J.; Roach, P.; Alexandrov, T. Proceedings of the National Academy of Sciences, Vol. 109, Issue 26 https://doi.org/10.1073/pnas.1203689109	journal	May 2012
The carbohydrate-active enzymes database (CAZy) in 2013 Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1178	journal	November 2013
QIIME allows analysis of high-throughput community sequencing data Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse Nature Methods, Vol. 7, Issue 5 https://doi.org/10.1038/nmeth.f.303	journal	April 2010
The microbiome of uncontacted Amerindians Clemente, Jose C.; Pehrsson, Erica C.; Blaser, Martin J. Science Advances, Vol. 1, Issue 3 https://doi.org/10.1126/sciadv.1500183	journal	April 2015
Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies Song, Se Jin; Amir, Amnon; Metcalf, Jessica L. mSystems, Vol. 1, Issue 3 https://doi.org/10.1128/mSystems.00021-16	journal	May 2016
Colicin E2 Production and Release by Escherichia coli K12 and Other Enterobacteriaceae Pugsley, A. P.; Goldzahl, N.; Barker, R. M. Microbiology, Vol. 131, Issue 10 https://doi.org/10.1099/00221287-131-10-2673	journal	October 1985
HMMER web server: interactive sequence similarity searching Finn, R. D.; Clements, J.; Eddy, S. R. Nucleic Acids Research, Vol. 39, Issue suppl https://doi.org/10.1093/nar/gkr367	journal	May 2011
EMPeror: a tool for visualizing high-throughput microbial community data Vázquez-Baeza, Yoshiki; Pirrung, Meg; Gonzalez, Antonio GigaScience, Vol. 2, Issue 1 https://doi.org/10.1186/2047-217X-2-16	journal	November 2013
Population-level analysis of gut microbiome variation Falony, Gwen; Joossens, Marie; Vieira-Silva, Sara Science, Vol. 352, Issue 6285 https://doi.org/10.1126/science.aad3503	journal	April 2016
Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range Henderson, Gemma; Cox, Faith; Ganesh, Siva Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep14567	journal	October 2015
Dynamics of the human gut microbiome in inflammatory bowel disease Halfvarson, Jonas; Brislawn, Colin J.; Lamendella, Regina Nature Microbiology, Vol. 2, Issue 5 https://doi.org/10.1038/nmicrobiol.2017.4	journal	February 2017
The control and consequences of bacterial fermentation in the human colon Cummings, J. H.; Macfarlane, G. T. Journal of Applied Bacteriology, Vol. 70, Issue 6 https://doi.org/10.1111/j.1365-2672.1991.tb02739.x	journal	June 1991
Searching molecular structure databases with tandem mass spectra using CSI:FingerID Dührkop, Kai; Shen, Huibin; Meusel, Marvin Proceedings of the National Academy of Sciences, Vol. 112, Issue 41 https://doi.org/10.1073/pnas.1509788112	journal	September 2015
Commensal bacteria make GPCR ligands that mimic human signalling molecules Cohen, Louis J.; Esterhazy, Daria; Kim, Seong-Hwan Nature, Vol. 549, Issue 7670 https://doi.org/10.1038/nature23874	journal	August 2017
Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis Xia, Jianguo; Wishart, David S. Current Protocols in Bioinformatics, Vol. 55, Issue 1 https://doi.org/10.1002/cpbi.11	journal	September 2016
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities Lozupone, C.; Knight, R. Applied and Environmental Microbiology, Vol. 71, Issue 12 https://doi.org/10.1128/AEM.71.12.8228-8235.2005	journal	December 2005
Cohabiting family members share microbiota with one another and with their dogs Song, Se Jin; Lauber, Christian; Costello, Elizabeth K. eLife, Vol. 2 https://doi.org/10.7554/eLife.00458	journal	April 2013
Evaluation of Normalization Methods to Pave the Way Towards Large-Scale LC-MS-Based Metabolomics Profiling Experiments Ejigu, Bedilu Alamirie; Valkenborg, Dirk; Baggerman, Geert OMICS: A Journal of Integrative Biology, Vol. 17, Issue 9 https://doi.org/10.1089/omi.2013.0010	journal	September 2013
Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology Gibson, Molly K.; Forsberg, Kevin J.; Dantas, Gautam The ISME Journal, Vol. 9, Issue 1 https://doi.org/10.1038/ismej.2014.106	journal	July 2014
Polyunsaturated fatty acid saturation by gut lactic acid bacteria affecting host lipid composition Kishino, S.; Takeuchi, M.; Park, S. -B. Proceedings of the National Academy of Sciences, Vol. 110, Issue 44 https://doi.org/10.1073/pnas.1312937110	journal	October 2013
An Ordination of the Upland Forest Communities of Southern Wisconsin Bray, J. Roger; Curtis, J. T. Ecological Monographs, Vol. 27, Issue 4 https://doi.org/10.2307/1942268	journal	February 1957
Molecular Networking as a Dereplication Strategy Yang, Jane Y.; Sanchez, Laura M.; Rath, Christopher M. Journal of Natural Products, Vol. 76, Issue 9 https://doi.org/10.1021/np400413s	journal	August 2013
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea McDonald, Daniel; Price, Morgan N.; Goodrich, Julia The ISME Journal, Vol. 6, Issue 3 https://doi.org/10.1038/ismej.2011.139	journal	December 2011
Quantitative and Qualitative Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities Lozupone, C. A.; Hamady, M.; Kelley, S. T. Applied and Environmental Microbiology, Vol. 73, Issue 5 https://doi.org/10.1128/AEM.01996-06	journal	January 2007
Bringing the Dynamic Microbiome to Life with Animations Vázquez-Baeza, Yoshiki; Gonzalez, Antonio; Smarr, Larry Cell Host & Microbe, Vol. 21, Issue 1 https://doi.org/10.1016/j.chom.2016.12.009	journal	January 2017
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data Pluskal, Tomáš; Castillo, Sandra; Villar-Briones, Alejandro BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-395	journal	July 2010
Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton Apprill, A.; McNally, S.; Parsons, R. Aquatic Microbial Ecology, Vol. 75, Issue 2 https://doi.org/10.3354/ame01753	journal	June 2015
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
Trends in GPCR drug discovery: new agents, targets and indications Hauser, Alexander S.; Attwood, Misty M.; Rask-Andersen, Mathias Nature Reviews Drug Discovery, Vol. 16, Issue 12 https://doi.org/10.1038/nrd.2017.178	journal	October 2017
Escherichia coli Induces DNA Double-Strand Breaks in Eukaryotic Cells Nougayrede, J. -P. Science, Vol. 313, Issue 5788 https://doi.org/10.1126/science.1127059	journal	August 2006
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
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets Wu, Yu-Wei; Simmons, Blake A.; Singer, Steven W. Bioinformatics, Vol. 32, Issue 4 https://doi.org/10.1093/bioinformatics/btv638	journal	October 2015
Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes Jiang, Lingjing; Amir, Amnon; Morton, James T. mSystems, Vol. 2, Issue 6 https://doi.org/10.1128/mSystems.00092-17	journal	November 2017
Challenges of self-reported medical conditions and electronic medical records among members of a large military cohort Smith, Besa; Chu, Laura K.; Smith, Tyler C. BMC Medical Research Methodology, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2288-8-37	journal	June 2008
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota Kaoutari, Abdessamad El; Armougom, Fabrice; Gordon, Jeffrey I. Nature Reviews Microbiology, Vol. 11, Issue 7 https://doi.org/10.1038/nrmicro3050	journal	June 2013
Conservation evaluation and phylogenetic diversity Faith, Daniel P. Biological Conservation, Vol. 61, Issue 1 https://doi.org/10.1016/0006-3207(92)91201-3	journal	January 1992
Subsistence strategies in traditional societies distinguish gut microbiomes Obregon-Tito, Alexandra J.; Tito, Raul Y.; Metcalf, Jessica Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms7505	journal	March 2015
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity Zhernakova, Alexandra; Kurilshikov, Alexander; Bonder, Marc Jan Science, Vol. 352, Issue 6285 https://doi.org/10.1126/science.aad3369	journal	April 2016
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
The WHO World Health Report 2001 on mental health Saraceno, Benedetto Epidemiologia e Psichiatria Sociale, Vol. 11, Issue 2 https://doi.org/10.1017/S1121189X00005546	journal	June 2002
Oscillospira and related bacteria - From metagenomic species to metabolic features : Metabolism of Oscillospira Gophna, Uri; Konikoff, Tom; Nielsen, Henrik Bjørn Environmental Microbiology, Vol. 19, Issue 3 https://doi.org/10.1111/1462-2920.13658	journal	February 2017
Notes on Continuous Stochastic Phenomena Moran, P. A. P. Biometrika, Vol. 37, Issue 1-2 https://doi.org/10.1093/biomet/37.1-2.17	journal	January 1950
PLS-regression: a basic tool of chemometrics Wold, Svante; Sjöström, Michael; Eriksson, Lennart Chemometrics and Intelligent Laboratory Systems, Vol. 58, Issue 2 https://doi.org/10.1016/S0169-7439(01)00155-1	journal	October 2001
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
Normalization and microbial differential abundance strategies depend upon data characteristics Weiss, Sophie; Xu, Zhenjiang Zech; Peddada, Shyamal Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0237-y	journal	March 2017
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
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
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
Escherichia coli Producing Colibactin Triggers Premature and Transmissible Senescence in Mammalian Cells Secher, Thomas; Samba-Louaka, Ascel; Oswald, Eric PLoS ONE, Vol. 8, Issue 10 https://doi.org/10.1371/journal.pone.0077157	journal	October 2013
FragGeneScan: predicting genes in short and error-prone reads Rho, Mina; Tang, Haixu; Ye, Yuzhen Nucleic Acids Research, Vol. 38, Issue 20 https://doi.org/10.1093/nar/gkq747	journal	August 2010
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking Wang, Mingxun; Carver, Jeremy J.; Phelan, Vanessa V. Nature Biotechnology, Vol. 34, Issue 8 https://doi.org/10.1038/nbt.3597	journal	August 2016
Accelerated Profile HMM Searches Eddy, Sean R. PLoS Computational Biology, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pcbi.1002195	journal	October 2011
Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra Gurevich, Alexey; Mikheenko, Alla; Shlemov, Alexander Nature Microbiology, Vol. 3, Issue 3 https://doi.org/10.1038/s41564-017-0094-2	journal	January 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
Human gut microbiome viewed across age and geography Yatsunenko, Tanya; Rey, Federico E.; Manary, Mark J. Nature, Vol. 486, Issue 7402 https://doi.org/10.1038/nature11053	journal	May 2012
Fast gapped-read alignment with Bowtie 2 Langmead, Ben; Salzberg, Steven L. Nature Methods, Vol. 9, Issue 4 https://doi.org/10.1038/nmeth.1923	journal	March 2012
Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist Cohen, Louis J.; Kang, Hahk-Soo; Chu, John Proceedings of the National Academy of Sciences, Vol. 112, Issue 35 https://doi.org/10.1073/pnas.1508737112	journal	August 2015
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Shannon, P. Genome Research, Vol. 13, Issue 11 https://doi.org/10.1101/gr.1239303	journal	November 2003
Unweighted UniFrac distances McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam Figshare https://doi.org/10.6084/m9.figshare.6131024	dataset	January 2018
Altered fecal microbiota composition in patients with major depressive disorder Jiang, Haiyin; Ling, Zongxin; Zhang, Yonghua Brain, Behavior, and Immunity, Vol. 48 https://doi.org/10.1016/j.bbi.2015.03.016	journal	August 2015
A power primer. Cohen, Jacob Psychological Bulletin, Vol. 112, Issue 1 https://doi.org/10.1037/0033-2909.112.1.155	journal	January 1992
Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI) Sumner, Lloyd W.; Amberg, Alexander; Barrett, Dave Metabolomics, Vol. 3, Issue 3 https://doi.org/10.1007/s11306-007-0082-2	journal	September 2007
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
Diet rapidly and reproducibly alters the human gut microbiome David, Lawrence A.; Maurice, Corinne F.; Carmody, Rachel N. Nature, Vol. 505, Issue 7484 https://doi.org/10.1038/nature12820	journal	December 2013
Controlling False Discoveries in Multidimensional Directional Decisions, with Applications to Gene Expression Data on Ordered Categories Guo, Wenge; Sarkar, Sanat K.; Peddada, Shyamal D. Biometrics, Vol. 66, Issue 2 https://doi.org/10.1111/j.1541-0420.2009.01292.x	journal	July 2009
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A. The ISME Journal, Vol. 6, Issue 8 https://doi.org/10.1038/ismej.2012.8	journal	March 2012
Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism Zheng, P.; Zeng, B.; Zhou, C. Molecular Psychiatry, Vol. 21, Issue 6 https://doi.org/10.1038/mp.2016.44	journal	April 2016
OpenMS: a flexible open-source software platform for mass spectrometry data analysis Röst, Hannes L.; Sachsenberg, Timo; Aiche, Stephan Nature Methods, Vol. 13, Issue 9 https://doi.org/10.1038/nmeth.3959	journal	August 2016
Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder Lin, Ping; Ding, Bingyu; Feng, Chunyan Journal of Affective Disorders, Vol. 207 https://doi.org/10.1016/j.jad.2016.09.051	journal	January 2017
Random Forests Breiman, Leo Machine Learning, Vol. 45, Issue 1, p. 5-32 https://doi.org/10.1023/A:1010933404324	journal	January 2001
Core fecal microbiota of domesticated herbivorous ruminant, hindgut fermenters, and monogastric animals O’ Donnell, Michelle M.; Harris, Hugh M. B.; Ross, R. Paul MicrobiologyOpen, Vol. 6, Issue 5 https://doi.org/10.1002/mbo3.509	journal	August 2017
Neue Begründung der Theorie quadratischer Formen von unendlichvielen Veränderlichen. Hellinger, E. Journal für die reine und angewandte Mathematik (Crelles Journal), Vol. 1909, Issue 136 https://doi.org/10.1515/crll.1909.136.210	journal	July 1909
Altered fecal microbiota composition in the Flinders sensitive line rat model of depression Tillmann, Sandra; Abildgaard, Anders; Winther, Gudrun Psychopharmacology, Vol. 236, Issue 5 https://doi.org/10.1007/s00213-018-5094-2	journal	November 2018
Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method Das, Sayak; Roy, Goshaidas; Najar, Ishfaq Nabi Folia Microbiologica, Vol. 66, Issue 3 https://doi.org/10.1007/s12223-021-00859-z	journal	March 2021
Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth Shao, Yan; Forster, Samuel C.; Tsaliki, Evdokia Nature, Vol. 574, Issue 7776 https://doi.org/10.1038/s41586-019-1560-1	journal	September 2019
Reconstruction of ancient microbial genomes from the human gut Wibowo, Marsha C.; Yang, Zhen; Borry, Maxime Nature, Vol. 594, Issue 7862 https://doi.org/10.1038/s41586-021-03532-0	journal	May 2021
miRNALoc: predicting miRNA subcellular localizations based on principal component scores of physico-chemical properties and pseudo compositions of di-nucleotides Meher, Prabina Kumar; Satpathy, Subhrajit; Rao, Atmakuri Ramakrishna Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-71381-4	journal	September 2020
A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology Calhoun, Sara; Bell, Tisza Ann Szeremy; Dahlin, Lukas R. Communications Biology, Vol. 4, Issue 1 https://doi.org/10.1038/s42003-021-01859-y	journal	March 2021
A new method for non-parametric multivariate analysis of variance Anderson, Marti J. Austral Ecology, Vol. 26, Issue 1 https://doi.org/10.1046/j.1442-9993.2001.01070.x	journal	February 2001
Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea Kangale, Luis Johnson; Levasseur, Anthony; Raoult, Didier Microbiology Resource Announcements, Vol. 10, Issue 5 https://doi.org/10.1128/mra.00297-20	journal	February 2021
The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change Fouquier, Jennifer; Moreno Huizar, Nancy; Donnelly, Jody mSystems, Vol. 6, Issue 2 https://doi.org/10.1128/msystems.00848-20	journal	April 2021
Notes on Continuous Stochastic Phenomena Moran, P. A. P. Biometrika, Vol. 37, Issue 1/2 https://doi.org/10.2307/2332142	journal	June 1950
Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range Henderson, Gemma; Cox, Faith; Ganesh, Siva ETH Zurich https://doi.org/10.3929/ethz-b-000164426	text	January 2015
OpenMS: a flexible open-source software platform for mass spectrometry data analysis Röst, Hannes L.; Sachsenberg, Timo; Aiche, Stephan Nature Publishing Group https://doi.org/10.5167/uzh-131611	text	January 2016
Unweighted UniFrac distances McDonald, Daniel; McDonald, Daniel; Robbins-Pianka, Adam figshare https://doi.org/10.6084/m9.figshare.6131024.v1	dataset	January 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
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
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
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
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
A new method for non-parametric multivariate analysis of variance Anderson, Marti J. Austral Ecology, Vol. 26, Issue 1 https://doi.org/10.1111/j.1442-9993.2001.tb00081.x	journal	February 2001
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking M., Waters, Katrina; Yao, Peng,; L., McPhail, Kerry The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/dd92-mf79	text	January 2016
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

Cited By (43)

Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales of ecological data Washburne, Alex D.; Silverman, Justin D.; Morton, James T. Ecological Monographs, Vol. 89, Issue 2 https://doi.org/10.1002/ecm.1353	journal	February 2019
You are what you eat: diet, health and the gut microbiota Zmora, Niv; Suez, Jotham; Elinav, Eran Nature Reviews Gastroenterology & Hepatology, Vol. 16, Issue 1 https://doi.org/10.1038/s41575-018-0061-2	journal	September 2018
Clinical metagenomics Chiu, Charles Y.; Miller, Steven A. Nature Reviews Genetics, Vol. 20, Issue 6 https://doi.org/10.1038/s41576-019-0113-7	journal	March 2019
Synthetic ecology of the human gut microbiota Vrancken, Gino; Gregory, Ann C.; Huys, Geert R. B. Nature Reviews Microbiology, Vol. 17, Issue 12 https://doi.org/10.1038/s41579-019-0264-8	journal	October 2019
Global chemical effects of the microbiome include new bile-acid conjugations Quinn, Robert A.; Melnik, Alexey V.; Vrbanac, Alison Nature, Vol. 579, Issue 7797 https://doi.org/10.1038/s41586-020-2047-9	journal	February 2020
Regional variation limits applications of healthy gut microbiome reference ranges and disease models He, Yan; Wu, Wei; Zheng, Hui-Min Nature Medicine, Vol. 24, Issue 10 https://doi.org/10.1038/s41591-018-0164-x	journal	August 2018
The microbiome, cancer, and cancer therapy Helmink, Beth A.; Khan, M. A. Wadud; Hermann, Amanda Nature Medicine, Vol. 25, Issue 3 https://doi.org/10.1038/s41591-019-0377-7	journal	March 2019
Defining Dysbiosis for a Cluster of Chronic Diseases Wilkins, Lamont J.; Monga, Manoj; Miller, Aaron W. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-49452-y	journal	September 2019
Open Humans: A platform for participant-centered research and personal data exploration Greshake Tzovaras, Bastian; Angrist, Misha; Arvai, Kevin GigaScience, Vol. 8, Issue 6 https://doi.org/10.1093/gigascience/giz076	journal	June 2019
Confounding factors in the effect of gut microbiota on bone density Aurora, Rajeev Rheumatology, Vol. 58, Issue 12 https://doi.org/10.1093/rheumatology/kez347	journal	August 2019
A Lot on Your Plate? Well-to-Well Contamination as an Additional Confounder in Microbiome Sequence Analyses Walker, Alan W. mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/msystems.00362-19	journal	August 2019
Human Skin, Oral, and Gut Microbiomes Predict Chronological Age Huang, Shi; Haiminen, Niina; Carrieri, Anna-Paola mSystems, Vol. 5, Issue 1 https://doi.org/10.1128/msystems.00630-19	journal	February 2020
Racial Differences in the Oral Microbiome: Data from Low-Income Populations of African Ancestry and European Ancestry Yang, Yaohua; Zheng, Wei; Cai, Qiuyin mSystems, Vol. 4, Issue 6 https://doi.org/10.1128/msystems.00639-19	journal	December 2019
Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension Marques, Francine Z.; Jama, Hamdi A.; Tsyganov, Kirill Hypertension, Vol. 74, Issue 6 https://doi.org/10.1161/hypertensionaha.119.13079	journal	December 2019
Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny Amato, Katherine R.; Mallott, Elizabeth K.; McDonald, Daniel Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1807-z	journal	October 2019
Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity Kaplan, Robert C.; Wang, Zheng; Usyk, Mykhaylo Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1831-z	journal	November 2019
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads Sanders, Jon G.; Nurk, Sergey; Salido, Rodolfo A. Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1834-9	journal	October 2019
tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies Liao, Tianhua; Wei, Yuchen; Luo, Mingjing Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1871-4	journal	December 2019
Daylight exposure modulates bacterial communities associated with household dust Fahimipour, Ashkaan K.; Hartmann, Erica M.; Siemens, Andrew Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0559-4	journal	October 2018
Framing the discussion of microorganisms as a facet of social equity in human health Ishaq, Suzanne L.; Rapp, Maurisa; Byerly, Risa PLOS Biology, Vol. 17, Issue 11 https://doi.org/10.1371/journal.pbio.3000536	journal	November 2019
Maturation of Gut Microbiota and Circulating Regulatory T Cells and Development of IgE Sensitization in Early Life Ruohtula, Terhi; de Goffau, Marcus C.; Nieminen, Janne K. Frontiers in Immunology, Vol. 10 https://doi.org/10.3389/fimmu.2019.02494	journal	October 2019
Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome Rodionov, Dmitry A.; Arzamasov, Aleksandr A.; Khoroshkin, Matvei S. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01316	journal	June 2019
MicroRNAs in Tumor Cell Metabolism: Roles and Therapeutic Opportunities Pedroza-Torres, Abraham; Romero-Córdoba, Sandra L.; Justo-Garrido, Montserrat Frontiers in Oncology, Vol. 9 https://doi.org/10.3389/fonc.2019.01404	journal	December 2019
Systematic Review of Gut Microbiota and Major Depression Cheung, Stephanie G.; Goldenthal, Ariel R.; Uhlemann, Anne-Catrin Frontiers in Psychiatry, Vol. 10 https://doi.org/10.3389/fpsyt.2019.00034	journal	February 2019
A Review of Traumatic Brain Injury and the Gut Microbiome: Insights into Novel Mechanisms of Secondary Brain Injury and Promising Targets for Neuroprotection Zhu, Caroline; Grandhi, Ramesh; Patterson, Thomas Brain Sciences, Vol. 8, Issue 6 https://doi.org/10.3390/brainsci8060113	journal	June 2018
In Vitro Evaluation of Different Prebiotics on the Modulation of Gut Microbiota Composition and Function in Morbid Obese and Normal-Weight Subjects Nogacka, Alicja M.; Salazar, Nuria; Arboleya, Silvia International Journal of Molecular Sciences, Vol. 21, Issue 3 https://doi.org/10.3390/ijms21030906	journal	January 2020
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview Sen, Partho; Orešič, Matej Metabolites, Vol. 9, Issue 2 https://doi.org/10.3390/metabo9020022	journal	January 2019
The neuroactive potential of the human gut microbiota in quality of life and depression Valles-Colomer, Mireia; Falony, Gwen; Darzi, Youssef Nature Microbiology, Vol. 4, Issue 4 https://doi.org/10.1038/s41564-018-0337-x	journal	February 2019
FEAST: fast expectation-maximization for microbial source tracking Shenhav, Liat; Thompson, Mike; Joseph, Tyler A. Nature Methods, Vol. 16, Issue 7 https://doi.org/10.1038/s41592-019-0431-x	journal	June 2019
Gut microbiota and obesity: An opportunity to alter obesity through faecal microbiota transplant (FMT) Lee, Patrick; Yacyshyn, Bruce R.; Yacyshyn, Mary B. Diabetes, Obesity and Metabolism, Vol. 21, Issue 3 https://doi.org/10.1111/dom.13561	journal	November 2018
Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease Mills, Robert H.; Vázquez-Baeza, Yoshiki; Zhu, Qiyun mSystems, Vol. 4, Issue 1 https://doi.org/10.1128/msystems.00337-18	journal	February 2019
The Microbiota-Gut-Brain Axis Cryan, John F.; O'Riordan, Kenneth J.; Cowan, Caitlin S. M. Physiological Reviews, Vol. 99, Issue 4 https://doi.org/10.1152/physrev.00018.2018	journal	October 2019
Recent advances in modulating the microbiome Quigley, Eamonn M. M.; Gajula, Prianka F1000Research, Vol. 9 https://doi.org/10.12688/f1000research.20204.1	journal	January 2020
16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses Woloszynek, Stephen; Zhao, Zhengqiao; Chen, Jian PLOS Computational Biology, Vol. 15, Issue 2 https://doi.org/10.1371/journal.pcbi.1006721	journal	February 2019
Clinician Guide to Microbiome Testing Staley, Christopher; Kaiser, Thomas; Khoruts, Alexander Digestive Diseases and Sciences, Vol. 63, Issue 12 https://doi.org/10.1007/s10620-018-5299-6	journal	September 2018
GABA-modulating bacteria of the human gut microbiota Strandwitz, Philip; Kim, Ki Hyun; Terekhova, Darya Nature Microbiology, Vol. 4, Issue 3 https://doi.org/10.1038/s41564-018-0307-3	journal	December 2018
Striped UniFrac: enabling microbiome analysis at unprecedented scale McDonald, Daniel; Vázquez-Baeza, Yoshiki; Koslicki, David Nature Methods, Vol. 15, Issue 11 https://doi.org/10.1038/s41592-018-0187-8	journal	October 2018
Identifying and Predicting Novelty in Microbiome Studies Su, Xiaoquan; Jing, Gongchao; McDonald, Daniel mBio, Vol. 9, Issue 6 https://doi.org/10.1128/mbio.02099-18	journal	December 2018
Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults de la Cuesta-Zuluaga, Jacobo; Kelley, Scott T.; Chen, Yingfeng mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/msystems.00261-19	journal	August 2019
Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration Leeming, Emily R.; Johnson, Abigail J.; Spector, Tim D. Nutrients, Vol. 11, Issue 12 https://doi.org/10.3390/nu11122862	journal	November 2019
Citizen science to further precision medicine: from vision to implementation Petersen, Carolyn; Austin, Robin R.; Backonja, Uba JAMIA Open, Vol. 3, Issue 1 https://doi.org/10.1093/jamiaopen/ooz060	journal	December 2019
Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria Cekanaviciute, Egle; Pröbstel, Anne-Katrin; Thomann, Anna mSystems, Vol. 3, Issue 6 https://doi.org/10.1128/msystems.00083-18	journal	October 2018
Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data Pendegraft, Amanda H.; Guo, Boyi; Yi, Nengjun PLOS ONE, Vol. 14, Issue 8 https://doi.org/10.1371/journal.pone.0220961	journal	August 2019