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Showing papers by "Jeroen Raes published in 2010"


Journal ArticleDOI
04 Mar 2010-Nature
TL;DR: The Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals are described, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species.
Abstract: To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, ~150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively

9,268 citations


Journal ArticleDOI
TL;DR: SmashCommunity provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple meetagenomes and to produce intuitive visual representations of such analyses.
Abstract: Summary: SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It supports state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction. It provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses. Availability: SmashCommunity source code and documentation are available at http://www.bork.embl.de/software/smash Contact: bork@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.

90 citations


Journal ArticleDOI
Pelin Yilmaz1, Renzo Kottmann1, Dawn Field2, Rob Knight3, James R. Cole4, Linda A. Amaral-Zettler5, Jack A. Gilbert6, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane7, Robert Vaughan7, Christopher I. Hunter7, Joonhong Park8, Norman Morrison9, Phillipe Rocca-Serra2, Peter Sterk, Mani Arumugam, Laura K. Baumgartner3, Bruce W. Birren10, Martin J. Blaser11, Vivien Bonazzi12, Peer Bork, Pier Luigi Buttigieg13, Patrick S. G. Chain14, Elizabeth K. Costello3, Heather Huot-Creasy15, Peter Dawyndt16, Todd Z. DeSantis17, Noah Fierer3, Jed A. Fuhrman18, Rachel E. Gallery19, Richard A. Gibbs20, Michelle G. Giglio15, Inigo San Gil21, Elizabeth M. Glass6, Antonio Gonzalez3, Jeffrey I. Gordon10, Robert P. Guralnick3, Wolfgang Hankeln13, Sarah Highlander22, Philip Hugenholtz23, Janet Jansson24, Jerry Kennedy3, Dan Knights3, Omry Koren22, Justin Kuczynski3, Nikos C. Kyrpides23, Robert Larsen3, Christian L. Lauber17, Teresa M. Legg3, Ruth E. Ley22, Catherine A. Lozupone3, Wolfgang Ludwig25, Donna Lyons17, Eamonn Maguire7, Barbara Methé26, Folker Meyer6, Sara Nakielny3, Karen E. Nelson26, Diana Nemergut27, Josh D. Neufeld28, Norman R. Pace3, Giriprakash Palanisamy3, Jörg Peplies29, Jane Peterson12, Joseph Petrosino22, Lita M. Proctor30, Jeroen Raes, Sujeevan Ratnasingham31, Jacques Ravel15, David A. Relman32, Susanna Assunta-Sansone7, Lynn M. Schriml15, Erica Sodergren33, Aymé Spor22, Jesse Stombaugh3, James M. Tiedje4, Doyle V. Ward10, George M. Weinstock33, Doug Wendel3, Owen White15, Andreas Wilke6, Jennifer Wortmann15, Frank Oliver Glöckner1 
TL;DR: The Genomic Standards Consortium's (GSC) Minimum Information about an ENvironmental Sequence (MIENS) standard for describing marker genes as discussed by the authors has been adopted for gene annotation.
Abstract: We present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

4 citations