Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Pelin Yilmaz,Pelin Yilmaz,Renzo Kottmann,Dawn Field,Rob Knight,Rob Knight,James R. Cole,Linda A. Amaral-Zettler,Jack A. Gilbert,Jack A. Gilbert,Jack A. Gilbert,Ilene Karsch-Mizrachi,Anjanette Johnston,Guy Cochrane,Robert Vaughan,Christopher I. Hunter,Joonhong Park,Norman Morrison,Philippe Rocca-Serra,Peter Sterk,Manimozhiyan Arumugam,Mark J. Bailey,Laura K. Baumgartner,Bruce W. Birren,Martin J. Blaser,Vivien Bonazzi,Timothy F. Booth,Peer Bork,Frederic D. Bushman,Pier Luigi Buttigieg,Pier Luigi Buttigieg,Patrick S. G. Chain,Patrick S. G. Chain,Patrick S. G. Chain,Emily S. Charlson,Elizabeth K. Costello,Heather Huot-Creasy,Peter Dawyndt,Todd Z. DeSantis,Noah Fierer,Jed A. Fuhrman,Rachel E. Gallery,Dirk Gevers,Richard A. Gibbs,Inigo San Gil,Antonio Gonzalez,Jeffrey I. Gordon,Robert P. Guralnick,Wolfgang Hankeln,Wolfgang Hankeln,Sarah K. Highlander,Philip Hugenholtz,Janet K. Jansson,Janet K. Jansson,Andrew L. Kau,Scott T. Kelley,Jerry Kennedy,Dan Knights,Omry Koren,Justin Kuczynski,Nikos C. Kyrpides,Robert Larsen,Christian L. Lauber,Teresa M. Legg,Ruth E. Ley,Catherine A. Lozupone,Wolfgang Ludwig,Donna Lyons,Eamonn Maguire,Barbara A. Methé,Folker Meyer,Brian D. Muegge,Sara Nakielny,Karen E. Nelson,Diana R. Nemergut,Josh D. Neufeld,Lindsay K. Newbold,Anna Oliver,Norman R. Pace,Giriprakash Palanisamy,Jörg Peplies,Joseph F. Petrosino,Lita M. Proctor,Elmar Pruesse,Elmar Pruesse,Christian Quast,Jeroen Raes,Sujeevan Ratnasingham,Jacques Ravel,David A. Relman,David A. Relman,Susanna Assunta-Sansone,Patrick D. Schloss,Lynn M. Schriml,Rohini Sinha,Michelle I. Smith,Erica Sodergren,Aymé Spor,Jesse Stombaugh,James M. Tiedje,Doyle V. Ward,George M. Weinstock,Doug Wendel,Owen White,Andrew S. Whiteley,Andreas Wilke,Jennifer R. Wortman,Tanya Yatsunenko,Frank Oliver Glöckner,Frank Oliver Glöckner +109 more
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TLDR
To establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, the minimum information about any (x) sequence is presented (MIxS).Abstract:
Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.read more
Citations
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Journal ArticleDOI
Ribosomal Database Project: data and tools for high throughput rRNA analysis
James R. Cole,Qiong Wang,Jordan A. Fish,Benli Chai,Donna M. McGarrell,Yanni Sun,C. Titus Brown,Andrea Porras-Alfaro,Cheryl R. Kuske,James M. Tiedje +9 more
TL;DR: RDP now includes a collection of fungal large subunit rRNA genes, and most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.
Journal ArticleDOI
A framework for human microbiome research
Barbara A. Methé,Karen E. Nelson,Mihai Pop,Heather Huot Creasy,Michelle G. Giglio,Curtis Huttenhower,Curtis Huttenhower,Dirk Gevers,Joseph F. Petrosino,Sahar Abubucker,Jonathan H. Badger,Asif T. Chinwalla,Ashlee M. Earl,Michael Fitzgerald,Robert S. Fulton,Kymberlie Hallsworth-Pepin,Elizabeth A. Lobos,Ramana Madupu,Vincent Magrini,John Martin,Makedonka Mitreva,Donna M. Muzny,Erica Sodergren,James Versalovic,Aye Wollam,Kim C. Worley,Jennifer R. Wortman,Sarah Young,Qiandong Zeng,Kjersti Aagaard,Olukemi O. Abolude,Emma Allen-Vercoe,Eric J. Alm,Eric J. Alm,Lucia Alvarado,Gary L. Andersen,Scott Anderson,Elizabeth L. Appelbaum,Harindra Arachchi,Gary C. Armitage,Cesar Arze,Tulin Ayvaz,Carl C. Baker,Lisa Begg,Tsegahiwot Belachew,Veena Bhonagiri,Monika Bihan,Martin J. Blaser,Toby Bloom,Vivien Bonazzi,Paul Brooks,Gregory A. Buck,Christian J. Buhay,Dana A. Busam,Joseph L. Campbell,Shane Canon,Brandi L. Cantarel,Patrick S. G. Chain,Patrick S. G. Chain,I. Min A. Chen,Lei Chen,Shaila Chhibba,Ken Chu,Dawn Ciulla,Jose C. Clemente,Sandra W. Clifton,Sean Conlan,Jonathan Crabtree,Mary A. Cutting,Noam J. Davidovics,Catherine C. Davis,Todd Z. DeSantis,Carolyn Deal,Kimberley D. Delehaunty,Floyd E. Dewhirst,Elena Deych,Yan Ding,David J. Dooling,Shannon Dugan,W. Michael Dunne,W. Michael Dunne,A. Scott Durkin,Robert C. Edgar,Rachel L. Erlich,Candace N. Farmer,Ruth M. Farrell,Karoline Faust,Michael Feldgarden,Victor Felix,Sheila Fisher,Anthony A. Fodor,Larry J. Forney,Leslie Foster,Valentina Di Francesco,Jonathan Friedman,Dennis C. Friedrich,Catrina Fronick,Lucinda Fulton,Hongyu Gao,Nathalia Garcia,Georgia Giannoukos,Christina Giblin,Maria Y. Giovanni,Jonathan M. Goldberg,Johannes B. Goll,Antonio Gonzalez,Allison D. Griggs,Sharvari Gujja,Brian J. Haas,Holli A. Hamilton,Emily L. Harris,Theresa A. Hepburn,Brandi Herter,Diane E. Hoffmann,Michael Holder,Clinton Howarth,Katherine H. Huang,Susan M. Huse,Jacques Izard,Janet K. Jansson,Huaiyang Jiang,Catherine Jordan,Vandita Joshi,James A. Katancik,Wendy A. Keitel,Scott T. Kelley,Cristyn Kells,Susan Kinder-Haake,Nicholas B. King,Rob Knight,Rob Knight,Dan Knights,Heidi H. Kong,Omry Koren,Sergey Koren,Karthik Kota,Christie Kovar,Nikos C. Kyrpides,Patricio S. La Rosa,Sandra L. Lee,Katherine P. Lemon,Niall Lennon,Cecil M. Lewis,Lora Lewis,Ruth E. Ley,Kelvin Li,Konstantinos Liolios,Bo Liu,Yue Liu,Chien Chi Lo,Catherine A. Lozupone,R. Dwayne Lunsford,Tessa Madden,Anup Mahurkar,Peter J. Mannon,Elaine R. Mardis,Victor M. Markowitz,Victor M. Markowitz,Konstantinos Mavrommatis,Jamison McCorrison,Daniel McDonald,Jean E. McEwen,Amy L. McGuire,Pamela McInnes,Teena Mehta,Kathie A. Mihindukulasuriya,Jason R. Miller,Patrick Minx,Irene Newsham,Chad Nusbaum,Michelle O'Laughlin,Joshua Orvis,Ioanna Pagani,Krishna Palaniappan,Shital M. Patel,Matthew D. Pearson,Jane Peterson,Mircea Podar,Craig Pohl,Katherine S. Pollard,Margaret Priest,Lita M. Proctor,Xiang Qin,Jeroen Raes,Jacques Ravel,Jeffrey G. Reid,Mina Rho,Rosamond Rhodes,Kevin Riehle,Maria C. Rivera,Beltran Rodriguez-Mueller,Yu-Hui Rogers,Matthew C. Ross,Carsten Russ,Ravi Sanka,Pamela Sankar,J. Fah Sathirapongsasuti,Jeffery A. Schloss,Patrick D. Schloss,Thomas M. Schmidt,Matthew B. Scholz,Lynn M. Schriml,Alyxandria M. Schubert,Nicola Segata,Julia A. Segre,William D. Shannon,Richard R. Sharp,Thomas J. Sharpton,Narmada Shenoy,Nihar U. Sheth,Gina A. Simone,Indresh Singh,Christopher Smillie,Jack D. Sobel,Daniel D. Sommer,Paul Spicer,Granger G. Sutton,Sean M. Sykes,Diana Tabbaa,Mathangi Thiagarajan,Chad Tomlinson,Manolito Torralba,Todd J. Treangen,Rebecca Truty,Tatiana A. Vishnivetskaya,Jason Walker,Lu Wang,Zhengyuan Wang,Doyle V. Ward,Wesley C. Warren,Mark A. Watson,Christopher Wellington,Kris A. Wetterstrand,James R. White,Katarzyna Wilczek-Boney,Yuan Qing Wu,Kristine M. Wylie,Todd Wylie,Chandri Yandava,Liang Ye,Yuzhen Ye,Shibu Yooseph,Bonnie P. Youmans,Lan Zhang,Yanjiao Zhou,Yiming Zhu,Laurie Zoloth,Jeremy Zucker,Bruce W. Birren,Richard A. Gibbs,Sarah K. Highlander,George M. Weinstock,Richard K. Wilson,Owen White +253 more
TL;DR: The Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomics data available to the scientific community as mentioned in this paper.
Journal ArticleDOI
Life in the “Plastisphere”: Microbial Communities on Plastic Marine Debris
TL;DR: Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer, implying that plastic serves as a novel ecological habitat in the open ocean.
Journal ArticleDOI
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
TL;DR: 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.
Journal ArticleDOI
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications.
Rolf Henrik Nilsson,Karl-Henrik Larsson,Andy F. S. Taylor,Johan Bengtsson-Palme,Johan Bengtsson-Palme,Thomas Stjernegaard Jeppesen,Dmitry Schigel,Peter G. Kennedy,Kathryn T. Picard,Frank Oliver Glöckner,Leho Tedersoo,Irja Saar,Urmas Kõljalg,Kessy Abarenkov +13 more
TL;DR: UNITE is a web-based database and sequence management environment for the molecular identification of fungi that targets the formal fungal barcode—the nuclear ribosomal internal transcribed spacer region—and offers all public fungal ITS sequences for reference.
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