Choice of molecular barcode will affect species prevalence but not bacterial community composition

Karen Lebret; Joanna Schroeder; Cecilia Balestreri; Andrea Highfield; Denise Cummings; Tim Smyth; Declan Schroeder

doi:10.1016/j.margen.2016.09.001

Choice of molecular barcode will affect species prevalence but not bacterial community composition

Karen Lebret, Joanna Schroeder, Cecilia Balestreri, Andrea Highfield, Denise Cummings, Tim Smyth, Declan Schroeder

Veterinary Population Medicine

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

Abstract

The rapid advancement of next generation sequencing protocols in recent years has led to the diversification in the methods used to study microbial communities; however, how comparable the data generated from these different methods are, remains unclear. In this study we compared the taxonomic composition and seasonal dynamics of the bacterial community determined by two distinct 16s amplicon sequencing protocols: sequencing of the V6 region of the 16s rRNA gene using 454 pyrosequencing vs the V4 region of the 16s rRNA gene using the Illumina Hiseq 2500 platform. Significant differences between relative abundances at all taxonomic levels were observed; however, their seasonal dynamics between phyla were largely consistent between methods. This study highlights that care must be taken when comparing datasets generated from different methods.

Original language	English (US)
Pages (from-to)	39-43
Number of pages	5
Journal	Marine Genomics
Volume	29
DOIs	https://doi.org/10.1016/j.margen.2016.09.001
State	Published - Oct 1 2016

Bibliographical note

Funding Information:
This study was funded by FP7 -OCEAN-2011 call, MicroB3 (grant number 287589 ) to D.S. and a post-doctoral research grant from the Swedish Research Council (Vetenskapsrådet; grant number 637-2014-6821 ) to K.L. We would also like to thank the University of Exeter sequencing service for their support and advice.

Publisher Copyright:
© 2016 The Authors

Keywords

16S
Illumina
Marine bacterial community
Pyrosequencing

Access

10.1016/j.margen.2016.09.001

OpenUrl availability

Full text

Cite this

@article{5946d78d33a14231b98a5f173f284e49,

title = "Choice of molecular barcode will affect species prevalence but not bacterial community composition",

abstract = "The rapid advancement of next generation sequencing protocols in recent years has led to the diversification in the methods used to study microbial communities; however, how comparable the data generated from these different methods are, remains unclear. In this study we compared the taxonomic composition and seasonal dynamics of the bacterial community determined by two distinct 16s amplicon sequencing protocols: sequencing of the V6 region of the 16s rRNA gene using 454 pyrosequencing vs the V4 region of the 16s rRNA gene using the Illumina Hiseq 2500 platform. Significant differences between relative abundances at all taxonomic levels were observed; however, their seasonal dynamics between phyla were largely consistent between methods. This study highlights that care must be taken when comparing datasets generated from different methods.",

keywords = "16S, Illumina, Marine bacterial community, Pyrosequencing",

author = "Karen Lebret and Joanna Schroeder and Cecilia Balestreri and Andrea Highfield and Denise Cummings and Tim Smyth and Declan Schroeder",

note = "Funding Information: This study was funded by FP7 -OCEAN-2011 call, MicroB3 (grant number 287589 ) to D.S. and a post-doctoral research grant from the Swedish Research Council (Vetenskapsr{\aa}det; grant number 637-2014-6821 ) to K.L. We would also like to thank the University of Exeter sequencing service for their support and advice. Publisher Copyright: {\textcopyright} 2016 The Authors",

year = "2016",

month = oct,

day = "1",

doi = "10.1016/j.margen.2016.09.001",

language = "English (US)",

volume = "29",

pages = "39--43",

journal = "Marine Genomics",

issn = "1874-7787",

publisher = "Elsevier",

}

TY - JOUR

T1 - Choice of molecular barcode will affect species prevalence but not bacterial community composition

AU - Lebret, Karen

AU - Schroeder, Joanna

AU - Balestreri, Cecilia

AU - Highfield, Andrea

AU - Cummings, Denise

AU - Smyth, Tim

AU - Schroeder, Declan

N1 - Funding Information: This study was funded by FP7 -OCEAN-2011 call, MicroB3 (grant number 287589 ) to D.S. and a post-doctoral research grant from the Swedish Research Council (Vetenskapsrådet; grant number 637-2014-6821 ) to K.L. We would also like to thank the University of Exeter sequencing service for their support and advice. Publisher Copyright: © 2016 The Authors

PY - 2016/10/1

Y1 - 2016/10/1

N2 - The rapid advancement of next generation sequencing protocols in recent years has led to the diversification in the methods used to study microbial communities; however, how comparable the data generated from these different methods are, remains unclear. In this study we compared the taxonomic composition and seasonal dynamics of the bacterial community determined by two distinct 16s amplicon sequencing protocols: sequencing of the V6 region of the 16s rRNA gene using 454 pyrosequencing vs the V4 region of the 16s rRNA gene using the Illumina Hiseq 2500 platform. Significant differences between relative abundances at all taxonomic levels were observed; however, their seasonal dynamics between phyla were largely consistent between methods. This study highlights that care must be taken when comparing datasets generated from different methods.

AB - The rapid advancement of next generation sequencing protocols in recent years has led to the diversification in the methods used to study microbial communities; however, how comparable the data generated from these different methods are, remains unclear. In this study we compared the taxonomic composition and seasonal dynamics of the bacterial community determined by two distinct 16s amplicon sequencing protocols: sequencing of the V6 region of the 16s rRNA gene using 454 pyrosequencing vs the V4 region of the 16s rRNA gene using the Illumina Hiseq 2500 platform. Significant differences between relative abundances at all taxonomic levels were observed; however, their seasonal dynamics between phyla were largely consistent between methods. This study highlights that care must be taken when comparing datasets generated from different methods.

KW - 16S

KW - Illumina

KW - Marine bacterial community

KW - Pyrosequencing

UR - http://www.scopus.com/inward/record.url?scp=84994099337&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84994099337&partnerID=8YFLogxK

U2 - 10.1016/j.margen.2016.09.001

DO - 10.1016/j.margen.2016.09.001

M3 - Article

C2 - 27650378

AN - SCOPUS:84994099337

SN - 1874-7787

VL - 29

SP - 39

EP - 43

JO - Marine Genomics

JF - Marine Genomics

ER -

Choice of molecular barcode will affect species prevalence but not bacterial community composition

Abstract

Bibliographical note

Keywords

Access

OpenUrl availability

Other files and links

Fingerprint

Cite this