A communal catalogue reveals Earth’s multiscale microbial diversity
Luke R. Thompson,Luke R. Thompson,Luke R. Thompson,Jon G. Sanders,Daniel McDonald,Amnon Amir,Joshua Ladau,Kenneth J. Locey,Robert J. Prill,Anupriya Tripathi,Sean M. Gibbons,Sean M. Gibbons,Gail Ackermann,Jose A. Navas-Molina,Stefan Janssen,Evguenia Kopylova,Yoshiki Vázquez-Baeza,Antonio Gonzalez,James T. Morton,Siavash Mirarab,Zhenjiang Zech Xu,Lingjing Jiang,Mohamed F. Haroon,Jad N. Kanbar,Qiyun Zhu,Se Jin Song,Tomasz Kosciolek,Nicholas A. Bokulich,Joshua P Lefler,Colin J. Brislawn,Gregory Humphrey,Sarah M. Owens,Jarrad T. Hampton-Marcell,Jarrad T. Hampton-Marcell,Donna Berg-Lyons,Valerie J. McKenzie,Noah Fierer,Noah Fierer,Jed A. Fuhrman,Aaron Clauset,Rick Stevens,Rick Stevens,Ashley Shade,Katherine S. Pollard,Kelly D. Goodwin,Janet K. Jansson,Jack A. Gilbert,Jack A. Gilbert,Rob Knight +48 more
TLDR
A meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project is presented, creating both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.Abstract:
Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.read more
Citations
More filters
Journal ArticleDOI
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
Nicholas A. Bokulich,Benjamin D. Kaehler,Jai Ram Rideout,Matthew R. Dillon,Evan Bolyen,Rob Knight,Gavin A. Huttley,J. Gregory Caporaso +7 more
TL;DR: The results illustrate the importance of parameter tuning for optimizing classifier performance, and the recommendations regarding parameter choices for these classifiers under a range of standard operating conditions are made.
Journal ArticleDOI
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
Jason Lloyd-Price,Jason Lloyd-Price,Cesar Arze,Ashwin N. Ananthakrishnan,Melanie Schirmer,Melanie Schirmer,Julian Avila-Pacheco,Tiffany W. Poon,Elizabeth Andrews,Nadim J. Ajami,Kevin S. Bonham,Kevin S. Bonham,Colin J. Brislawn,David Casero,Holly Courtney,Antonio Gonzalez,Thomas G. Graeber,A. Brantley Hall,Kathleen Lake,Carol J. Landers,Himel Mallick,Himel Mallick,Damian R. Plichta,Mahadev Prasad,Gholamali Rahnavard,Gholamali Rahnavard,Jenny S. Sauk,Dmitry Shungin,Dmitry Shungin,Yoshiki Vázquez-Baeza,Richard A. White,Jonathan Braun,Lee A. Denson,Lee A. Denson,Janet K. Jansson,Rob Knight,Subra Kugathasan,Dermot P.B. McGovern,Joseph F. Petrosino,Thaddeus S. Stappenbeck,Harland S. Winter,Clary B. Clish,Eric A. Franzosa,Hera Vlamakis,Ramnik J. Xavier,Ramnik J. Xavier,Ramnik J. Xavier,Curtis Huttenhower,Curtis Huttenhower +48 more
TL;DR: It is demonstrated that periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts, and integrative analysis identified microbial, biochemical, and host factors central to this dysregulation.
Journal ArticleDOI
A global atlas of the dominant bacteria found in soil
Manuel Delgado-Baquerizo,Manuel Delgado-Baquerizo,Angela M. Oliverio,Angela M. Oliverio,Tess E. Brewer,Tess E. Brewer,Alberto Benavent-González,David J. Eldridge,Richard D. Bardgett,Fernando T. Maestre,Brajesh K. Singh,Noah Fierer,Noah Fierer +12 more
TL;DR: This study narrows down the immense number of bacterial taxa to a “most wanted” list that will be fruitful targets for genomic and cultivation-based efforts aimed at improving the understanding of soil microbes and their contributions to ecosystem functioning.
Journal ArticleDOI
TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
TL;DR: TYGS, the Type (Strain) Genome Server, a user-friendly high-throughput web server for genome-based prokaryote taxonomy and analysis connected to a large, continuously growing database of genomic, taxonomic and nomenclatural information.
Journal ArticleDOI
Best practices for analysing microbiomes.
Rob Knight,Alison Vrbanac,Bryn C. Taylor,Alexander A. Aksenov,Chris Callewaert,Chris Callewaert,Justine W. Debelius,Antonio Gonzalez,Tomasz Kosciolek,Laura-Isobel McCall,Daniel McDonald,Alexey V. Melnik,James T. Morton,Jose Navas,Robert A. Quinn,Jon G. Sanders,Austin D. Swafford,Luke R. Thompson,Luke R. Thompson,Anupriya Tripathi,Zhenjiang Zech Xu,Jesse R. Zaneveld,Qiyun Zhu,J. Gregory Caporaso,Pieter C. Dorrestein,Pieter C. Dorrestein +25 more
TL;DR: This Review focuses on recent findings that suggest that operational taxonomic unit-based analyses should be replaced with new methods that are based on exact sequence variants, methods for integrating metagenomic and metabolomic data, and issues surrounding compositional data analysis.
References
More filters
Journal ArticleDOI
A mathematical theory of communication
TL;DR: This final installment of the paper considers the case where the signals or the messages or both are continuously variable, in contrast with the discrete nature assumed until now.
Journal ArticleDOI
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
TL;DR: This work presents some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.
Journal ArticleDOI
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast,Elmar Pruesse,Pelin Yilmaz,Jan Gerken,Timmy Schweer,Pablo Yarza,Jörg Peplies,Frank Oliver Glöckner +7 more
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
Related Papers (5)
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Evan Bolyen,Jai Ram Rideout,Matthew R. Dillon,Nicholas A. Bokulich,Christian C. Abnet,Gabriel A. Al-Ghalith,Harriet Alexander,Harriet Alexander,Eric J. Alm,Manimozhiyan Arumugam,Francesco Asnicar,Yang Bai,Jordan E. Bisanz,Kyle Bittinger,Asker Daniel Brejnrod,Colin J. Brislawn,C. Titus Brown,Benjamin J. Callahan,Andrés Mauricio Caraballo-Rodríguez,John Chase,Emily K. Cope,Ricardo Silva,Christian Diener,Pieter C. Dorrestein,Gavin M. Douglas,Daniel M. Durall,Claire Duvallet,Christian F. Edwardson,Madeleine Ernst,Madeleine Ernst,Mehrbod Estaki,Jennifer Fouquier,Julia M. Gauglitz,Sean M. Gibbons,Sean M. Gibbons,Deanna L. Gibson,Antonio Gonzalez,Kestrel Gorlick,Jiarong Guo,Benjamin Hillmann,Susan Holmes,Hannes Holste,Curtis Huttenhower,Curtis Huttenhower,Gavin A. Huttley,Stefan Janssen,Alan K. Jarmusch,Lingjing Jiang,Benjamin D. Kaehler,Benjamin D. Kaehler,Kyo Bin Kang,Kyo Bin Kang,Christopher R. Keefe,Paul Keim,Scott T. Kelley,Dan Knights,Irina Koester,Tomasz Kosciolek,Jorden Kreps,Morgan G. I. Langille,Joslynn S. Lee,Ruth E. Ley,Ruth E. Ley,Yong-Xin Liu,Erikka Loftfield,Catherine A. Lozupone,Massoud Maher,Clarisse Marotz,Bryan D Martin,Daniel McDonald,Lauren J. McIver,Lauren J. McIver,Alexey V. Melnik,Jessica L. Metcalf,Sydney C. Morgan,Jamie Morton,Ahmad Turan Naimey,Jose A. Navas-Molina,Jose A. Navas-Molina,Louis-Félix Nothias,Stephanie B. Orchanian,Talima Pearson,Samuel L. Peoples,Samuel L. Peoples,Daniel Petras,Mary L. Preuss,Elmar Pruesse,Lasse Buur Rasmussen,Adam R. Rivers,Michael S. Robeson,Patrick Rosenthal,Nicola Segata,Michael Shaffer,Arron Shiffer,Rashmi Sinha,Se Jin Song,John R. Spear,Austin D. Swafford,Luke R. Thompson,Luke R. Thompson,Pedro J. Torres,Pauline Trinh,Anupriya Tripathi,Peter J. Turnbaugh,Sabah Ul-Hasan,Justin J. J. van der Hooft,Fernando Vargas,Yoshiki Vázquez-Baeza,Emily Vogtmann,Max von Hippel,William A. Walters,Yunhu Wan,Mingxun Wang,Jonathan Warren,Kyle C. Weber,Kyle C. Weber,Charles H. D. Williamson,Amy D. Willis,Zhenjiang Zech Xu,Jesse R. Zaneveld,Yilong Zhang,Qiyun Zhu,Rob Knight,J. Gregory Caporaso +123 more