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Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes.
Department of Medicine, University of Connecticut Health Center, Farmington, CT, United States.
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2016 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, no April, article id 469Article in journal (Refereed) Published
Abstract [en]

Several metagenomic projects have been accomplished or are in progress. However, in most cases, it is not feasible to generate complete genomic assemblies of species from the metagenomic sequencing of a complex environment. Only a few studies have reported the reconstruction of bacterial genomes from complex metagenomes. In this work, Binning-Assembly approach has been proposed and demonstrated for the reconstruction of bacterial and viral genomes from 72 human gut metagenomic datasets. A total 1156 bacterial genomes belonging to 219 bacterial families and, 279 viral genomes belonging to 84 viral families could be identified. More than 80% complete draft genome sequences could be reconstructed for a total of 126 bacterial and 11 viral genomes. Selected draft assembled genomes could be validated with 99.8% accuracy using their ORFs. The study provides useful information on the assembly expected for a species given its number of reads and abundance. This approach along with spiking was also demonstrated to be useful in improving the draft assembly of a bacterial genome. The Binning-Assembly approach can be successfully used to reconstruct bacterial and viral genomes from multiple metagenomic datasets obtained from similar environments.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2016. Vol. 7, no April, article id 469
Keywords [en]
bacterial draft genomes, binning, genome assembly, metagenome, spiking, viral draft genomes
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:kth:diva-258003DOI: 10.3389/fmicb.2016.00469ISI: 000373978200001PubMedID: 27148174Scopus ID: 2-s2.0-84966393472OAI: oai:DiVA.org:kth-258003DiVA, id: diva2:1350774
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QC 20190913

Available from: 2019-09-12 Created: 2019-09-12 Last updated: 2019-09-13Bibliographically approved

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CiteExportLink to record
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Citation style
  • apa
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  • modern-language-association-8th-edition
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  • de-DE
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Output format
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