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https://doi.org/10.1371/journal.pone.0060811
Title: | Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences | Authors: | Ong S.H. Kukkillaya V.U. Wilm A. Lay C. Ho E.X.P. Low L. Hibberd M.L. Nagarajan N. |
Keywords: | RNA 16S 16S rRNA gene adult amplicon article bacterial gene computer model gene amplification genetic conservation human infant microbial community microbial identification nonhuman nucleotide sequence RNA analysis RNA sequence species identification unindexed sequence Adult Bacteria Child, Preschool Computational Biology Gastrointestinal Tract High-Throughput Nucleotide Sequencing Humans Metagenome Phylogeny RNA, Ribosomal, 16S Bacteria (microorganisms) Otus |
Issue Date: | 2013 | Citation: | Ong S.H., Kukkillaya V.U., Wilm A., Lay C., Ho E.X.P., Low L., Hibberd M.L., Nagarajan N. (2013). Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences. PLoS ONE 8 (4) : e60811. ScholarBank@NUS Repository. https://doi.org/10.1371/journal.pone.0060811 | Rights: | Attribution 4.0 International | Abstract: | The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing protocols are, however, limited by the fraction of the 16S rRNA gene that is interrogated and therefore limit the resolution and quality of the profiling. To address this, we present the design of a novel protocol for shotgun Illumina sequencing of the bacterial 16S rRNA gene, optimized to amplify more than 90% of sequences in the Greengenes database and with the ability to distinguish nearly twice as many species-level OTUs compared to existing protocols. Using several in silico and experimental datasets, we demonstrate that despite the presence of multiple variable and conserved regions, the resulting shotgun sequences can be used to accurately quantify the constituents of complex microbial communities. The reconstruction of a significant fraction of the 16S rRNA gene also enabled high precision (>90%) in species-level identification thereby opening up potential application of this approach for clinical microbial characterization. © 2013 Ong et al. | Source Title: | PLoS ONE | URI: | https://scholarbank.nus.edu.sg/handle/10635/161330 | ISSN: | 19326203 | DOI: | 10.1371/journal.pone.0060811 | Rights: | Attribution 4.0 International |
Appears in Collections: | Elements Staff Publications |
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