Showing papers by "Jeroen Raes published in 2010"
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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
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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
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Max Planck Society1, University of Oxford2, University of Colorado Boulder3, Michigan State University4, Marine Biological Laboratory5, Argonne National Laboratory6, European Bioinformatics Institute7, Yonsei University8, University of Manchester9, Massachusetts Institute of Technology10, New York University11, National Institutes of Health12, Jacobs University Bremen13, Los Alamos National Laboratory14, University of Maryland, Baltimore15, Ghent University16, Lawrence Berkeley National Laboratory17, University of Southern California18, National Ecological Observatory Network19, Human Genome Sequencing Center20, University of New Mexico21, Washington University in St. Louis22, Joint Genome Institute23, Baylor College of Medicine24, Cornell University25, Cooperative Institute for Research in Environmental Sciences26, Technische Universität München27, J. Craig Venter Institute28, University of Waterloo29, Oak Ridge National Laboratory30, National Science Foundation31, Vrije Universiteit Brussel32, Stanford University33
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