{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,9,17]],"date-time":"2022-09-17T05:49:39Z","timestamp":1663393779624},"reference-count":37,"publisher":"Walter de Gruyter GmbH","issue":"3","license":[{"start":{"date-parts":[[2016,6,25]],"date-time":"2016-06-25T00:00:00Z","timestamp":1466812800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>High throughput next generation sequencing technologies have enabled cultivation-independent approaches to study microbial\ncommunities in environmental samples. To date much of functional metagenomics has been limited to the gene or pathway\nlevel. Recent breakthroughs in metagenome binning have made it feasible to reconstruct high quality, individual microbial\ngenomes from complex communities with thousands of species. In this review we aim to compare several automated metagenome\nbinning software tools for their performance, and provide a practical guide for the metagenomics research community to\ncarry out successful binning analyses.<\/jats:p>","DOI":"10.1515\/itit-2016-0011","type":"journal-article","created":{"date-parts":[[2016,6,27]],"date-time":"2016-06-27T15:45:02Z","timestamp":1467042302000},"page":"133-139","source":"Crossref","is-referenced-by-count":6,"title":["Reconstructing single genomes from complex microbial communities"],"prefix":"10.1515","volume":"58","author":[{"given":"Dongwan D.","family":"Kang","sequence":"first","affiliation":[{"name":"Joint Genome Institute, Lawrence Berkeley National Laboratory, DOE, Walnut Creek, CA 94598, USA"}]},{"given":"Edward M.","family":"Rubin","sequence":"additional","affiliation":[{"name":"Joint Genome Institute, Lawrence Berkeley National Laboratory, DOE, Walnut Creek, CA 94598, USA"}]},{"given":"Zhong","family":"Wang","sequence":"additional","affiliation":[]}],"member":"374","published-online":{"date-parts":[[2016,6,25]]},"reference":[{"key":"ref471","doi-asserted-by":"crossref","first-page":"10314","DOI":"10.1371\/journal.pone.0010314","article-title":"One bacterial cell one complete genome PLoS","volume":"5","author":"Woyke","year":"2010","journal-title":"One"},{"key":"ref401","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1093\/bioinformatics\/bts723","article-title":"ALE : a generic as - sembly likelihood evaluation framework for assessing the ac - curacy of genome and metagenome assemblies","volume":"29","author":"Clark","year":"2013","journal-title":"Bioinformatics"},{"key":"ref61","first-page":"454","article-title":"Genomics of cellulosic biofuels","author":"Rubin","year":"2008","journal-title":"Nature"},{"key":"ref431","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nmeth1043","article-title":"Use of simulated data sets to evaluate the fidelity of metagenomic processing methods","volume":"4","author":"Mavromatis","year":"2007","journal-title":"Nat Methods"},{"key":"ref371","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1101\/gr.335003","article-title":"Evolutionary implications of microbial genome tetranucleotide frequency biases","volume":"13","author":"Pride","year":"2003","journal-title":"Genome Res"},{"key":"ref151","doi-asserted-by":"crossref","first-page":"2964","DOI":"10.1093\/bioinformatics\/btr520","article-title":"Bambus : scaffolding metagenomes Reconstructing single genomes from complex microbial communities DE GRUYTER OLDENBOURG Classification of metagenomic sequences : methods and challenges Brief","volume":"2","author":"Koren","year":"2011","journal-title":"Bioinformatics Bioinform"},{"key":"ref301","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1101\/gr.142315.112","article-title":"Time series community genomics analysis reveals rapid shifts in bacterial species strains and phage during infant gut colonization","volume":"23","author":"Sharon","year":"2013","journal-title":"Genome Res"},{"key":"ref81","first-page":"480","article-title":"Chavar - ria KL Metagenomic analysis of a permafrost mi - crobial community reveals a rapid response to thaw","author":"Mackelprang","year":"2011","journal-title":"Nature"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/nrmicro3262","article-title":"The microbial ecology of permafrost","volume":"12","author":"Jansson","year":"2014","journal-title":"Nat Rev Microbiol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1038\/nrg3182","article-title":"The human microbiome : at the interface of health and disease","volume":"13","author":"Cho","year":"2012","journal-title":"Nat Rev Genet"},{"key":"ref131","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1093\/bib\/bbs020","article-title":"Metagenomic analysis : the challenge of the data bo - nanza","volume":"13","author":"Hunter","year":"2012","journal-title":"Brief Bioinform"},{"key":"ref111","first-page":"304","article-title":"Environmental genome shotgun sequencing of the Sargasso Sea","author":"Venter","year":"2004","journal-title":"Science"},{"key":"ref441","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1186\/1471-2105-5-163","article-title":"TETRA : a web - service and a stand - alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences","volume":"5","author":"Teeling","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref51","first-page":"331","article-title":"Metagenomic discovery of biomass - degrading genes and genomes from cow rumen","author":"Hess","year":"2011","journal-title":"Science"},{"key":"ref261","first-page":"500","article-title":"Richness of human gut microbiome correlates with metabolic markers","author":"Le Chatelier","year":"2013","journal-title":"Nature"},{"key":"ref221","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/s12859-015-0473-8","article-title":"MBBC : an efficient approach for metagenomic binning based on clustering","volume":"16","author":"Wang","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"ref451","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/gb-2012-13-12-r122","article-title":"Ray Meta : scalable de novo metagenome assembly and profiling","volume":"13","author":"Boisvert","year":"2012","journal-title":"Genome Biol"},{"key":"ref381","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.1093\/molbev\/msp032","article-title":"Phylogenetic signals in DNA composition : limitations and prospects Biology","volume":"26","author":"Mrazek","year":"2009","journal-title":"Molecular and Evolution"},{"key":"ref231","first-page":"500","article-title":"Dietary intervention impact on gut microbial gene richness","author":"Cotillard","year":"2013","journal-title":"Nature"},{"key":"ref121","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1007\/s00248-006-9199-5","article-title":"Genotypic microbial com - munity profiling : a critical technical review","volume":"54","author":"Nocker","year":"2007","journal-title":"Microb Ecol"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/j.tig.2014.07.001","article-title":"Ten years of next - generation sequencing technology","volume":"30","author":"van Dijk","year":"2014","journal-title":"Trends Genet"},{"key":"ref331","first-page":"1165","article-title":"MetaBAT an efficient tool for accurately reconstructing single genomes from com - plex microbial communities Gut metagenome in European women with normal , impaired and diabetic glucose control","author":"Kang","year":"2015","journal-title":"Nature"},{"key":"ref171","first-page":"215","article-title":"Binning se - quences using very sparse labels within a metagenome BMC","volume":"9","author":"Chan","year":"2008","journal-title":"Bioinformatics"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"1688","DOI":"10.1038\/ismej.2012.10","article-title":"Metagenomic and metaproteomic insights into bacte - rial communities in leaf - cutter ant fungus gardens","volume":"6","author":"Aylward","year":"2012","journal-title":"ISME J"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1146\/annurev.genet.38.072902.091216","article-title":"Metage - nomics : genomic analysis of microbial communities","volume":"38","author":"Riesenfeld","year":"2004","journal-title":"Annu Rev Genet"},{"key":"ref141","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/gb-2014-15-3-r42","article-title":"A comprehen - sive evaluation of assembly scaffolding tools","volume":"15","author":"Hunt","year":"2014","journal-title":"Genome Biol"},{"key":"ref271","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/nbt.2579","article-title":"Genome sequences of rare uncultured bac - teria obtained by differential coverage binning of multiple metagenomes","volume":"31","author":"AlbertsenM","year":"2013","journal-title":"Nat Biotechnol"},{"key":"ref391","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1093\/nar\/gkr1204","article-title":"Unsupervised discov - ery of microbial population structure within metagenomes using nucleotide base composition","volume":"40","author":"Saeed","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref281","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1038\/nmeth.3103","article-title":"de Bruijn Binning metagenomic contigs by coverage and composition","volume":"11","author":"Alneberg","year":"2014","journal-title":"Nat Methods"},{"key":"ref461","first-page":"194","article-title":"Growing unculturable bacteria","author":"Stewart","year":"2012","journal-title":"J Bacteriol"},{"key":"ref311","first-page":"337","article-title":"Fermentation hydrogen and sulfur metabolism in multi - ple uncultivated bacterial phyla","author":"Wrighton","year":"2012","journal-title":"Science"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1128\/MMBR.68.4.669-685.2004","article-title":"Metagenomics : application of genomics to uncultured microorganisms","volume":"68","author":"Handelsman","year":"2004","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref161","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1111\/j.1462-2920.2004.00624.x","article-title":"Application of tetranucleotide frequencies for the as - 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