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

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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 languageEnglish (US)
Pages (from-to)39-43
Number of pages5
JournalMarine Genomics
StatePublished - 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


  • 16S
  • Illumina
  • Marine bacterial community
  • Pyrosequencing

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