Simultaneous pyrosequencing of the 16S rRNA, IncP-1 trfA, and merA genes

Peter Nikolai Holmsgaard; Søren Johannes Sørensen; Lars H. Hansen

doi:10.1016/j.mimet.2013.09.016

Simultaneous pyrosequencing of the 16S rRNA, IncP-1 trfA, and merA genes

Peter Nikolai Holmsgaard, Søren Johannes Sørensen, Lars H. Hansen

Microbiology

5 Citations (Scopus)

Abstract

The use of amplicon pyrosequencing makes it possible to produce thousands of sequences of the same gene at relatively low costs. Here we show that it is possible to simultaneously sequence the 16S rRNA gene, IncP-1 trfA gene and mercury reductase gene (merA) as a way for screening the diversity of several genes in the same samples. As a proof-of-concept two different soil samples and a wastewater sample were screened. Multiplexing identifiers (MIDs) and sequencing adapters were added to amplicons using a tailed PCR approach and the universal overhangs U1 and U2 for this approach were redesigned. Furthermore, this is the first time the IncP-1 plasmid diversity was studied by amplicon pyrosequencing and for this purpose a clustering threshold of 89% nucleotide sequence similarity was determined to differentiate the IncP-1 subgroups.

Original language	English
Journal	Journal of Microbiological Methods
Volume	95
Issue number	2
Pages (from-to)	280-284
Number of pages	5
ISSN	0167-7012
DOIs	https://doi.org/10.1016/j.mimet.2013.09.016
Publication status	Published - Nov 2013

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10.1016/j.mimet.2013.09.016

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title = "Simultaneous pyrosequencing of the 16S rRNA, IncP-1 trfA, and merA genes",

abstract = "The use of amplicon pyrosequencing makes it possible to produce thousands of sequences of the same gene at relatively low costs. Here we show that it is possible to simultaneously sequence the 16S rRNA gene, IncP-1 trfA gene and mercury reductase gene (merA) as a way for screening the diversity of several genes in the same samples. As a proof-of-concept two different soil samples and a wastewater sample were screened. Multiplexing identifiers (MIDs) and sequencing adapters were added to amplicons using a tailed PCR approach and the universal overhangs U1 and U2 for this approach were redesigned. Furthermore, this is the first time the IncP-1 plasmid diversity was studied by amplicon pyrosequencing and for this purpose a clustering threshold of 89% nucleotide sequence similarity was determined to differentiate the IncP-1 subgroups.",

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T1 - Simultaneous pyrosequencing of the 16S rRNA, IncP-1 trfA, and merA genes

AU - Holmsgaard, Peter Nikolai

AU - Sørensen, Søren Johannes

AU - Hansen, Lars H.

PY - 2013/11

Y1 - 2013/11

N2 - The use of amplicon pyrosequencing makes it possible to produce thousands of sequences of the same gene at relatively low costs. Here we show that it is possible to simultaneously sequence the 16S rRNA gene, IncP-1 trfA gene and mercury reductase gene (merA) as a way for screening the diversity of several genes in the same samples. As a proof-of-concept two different soil samples and a wastewater sample were screened. Multiplexing identifiers (MIDs) and sequencing adapters were added to amplicons using a tailed PCR approach and the universal overhangs U1 and U2 for this approach were redesigned. Furthermore, this is the first time the IncP-1 plasmid diversity was studied by amplicon pyrosequencing and for this purpose a clustering threshold of 89% nucleotide sequence similarity was determined to differentiate the IncP-1 subgroups.

AB - The use of amplicon pyrosequencing makes it possible to produce thousands of sequences of the same gene at relatively low costs. Here we show that it is possible to simultaneously sequence the 16S rRNA gene, IncP-1 trfA gene and mercury reductase gene (merA) as a way for screening the diversity of several genes in the same samples. As a proof-of-concept two different soil samples and a wastewater sample were screened. Multiplexing identifiers (MIDs) and sequencing adapters were added to amplicons using a tailed PCR approach and the universal overhangs U1 and U2 for this approach were redesigned. Furthermore, this is the first time the IncP-1 plasmid diversity was studied by amplicon pyrosequencing and for this purpose a clustering threshold of 89% nucleotide sequence similarity was determined to differentiate the IncP-1 subgroups.

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DO - 10.1016/j.mimet.2013.09.016

M3 - Journal article

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SN - 0167-7012

VL - 95

SP - 280

EP - 284

JO - Journal of Microbiological Methods

JF - Journal of Microbiological Methods

IS - 2

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Simultaneous pyrosequencing of the 16S rRNA, IncP-1 trfA, and merA genes

Abstract

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