Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.

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 fracti...

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Autores principales:	Swee Hoe Ong, Vinutha Uppoor Kukkillaya, Andreas Wilm, Christophe Lay, Eliza Xin Pei Ho, Louie Low, Martin Lloyd Hibberd, Niranjan Nagarajan
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/187921e45b354c67a91408306fbf8cf3
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spelling	oai:doaj.org-article:187921e45b354c67a91408306fbf8cf32021-11-18T07:50:17ZSpecies identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.1932-620310.1371/journal.pone.0060811https://doaj.org/article/187921e45b354c67a91408306fbf8cf32013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23579286/?tool=EBIhttps://doaj.org/toc/1932-6203The 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.Swee Hoe OngVinutha Uppoor KukkillayaAndreas WilmChristophe LayEliza Xin Pei HoLouie LowMartin Lloyd HibberdNiranjan NagarajanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 4, p e60811 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Swee Hoe Ong Vinutha Uppoor Kukkillaya Andreas Wilm Christophe Lay Eliza Xin Pei Ho Louie Low Martin Lloyd Hibberd Niranjan Nagarajan Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.
description	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.
format	article
author	Swee Hoe Ong Vinutha Uppoor Kukkillaya Andreas Wilm Christophe Lay Eliza Xin Pei Ho Louie Low Martin Lloyd Hibberd Niranjan Nagarajan
author_facet	Swee Hoe Ong Vinutha Uppoor Kukkillaya Andreas Wilm Christophe Lay Eliza Xin Pei Ho Louie Low Martin Lloyd Hibberd Niranjan Nagarajan
author_sort	Swee Hoe Ong
title	Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.
title_short	Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.
title_full	Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.
title_fullStr	Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.
title_full_unstemmed	Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.
title_sort	species identification and profiling of complex microbial communities using shotgun illumina sequencing of 16s rrna amplicon sequences.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/187921e45b354c67a91408306fbf8cf3
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Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.

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