Please use this identifier to cite or link to this item: 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
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
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