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Oral Biology pp 153-163 | Cite as

Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package

  • Blair LawleyEmail author
  • Gerald W. Tannock
Part of the Methods in Molecular Biology book series (MIMB, volume 1537)

Abstract

The study of microbial ecology has undergone a paradigm shift in recent years, with rapid advances in molecular and bioinformatic tools allowing researchers with wide-ranging interests and backgrounds access to community profiling methods. While these advances have undoubtedly led to exciting new understanding of many systems, the array of protocols available and the idiosyncrasies of particular approaches can lead to confusion or, at worst, erroneous interpretation of results. Here, we describe a workflow from raw 16S rRNA gene amplicon sequence data, generated on an Illumina MiSeq instrument, to microbial community taxonomy profiles and basic diversity measures. The workflow can be adapted to input from major sequence platforms and uses freely available open source software that can be implemented on a range of operating systems.

Key words

High-throughput sequencing 16S rRNA gene QIIME Microbial ecology Bioinformatics Sequence analysis Operational taxonomic unit (OTU) 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Department of Microbiology and ImmunologyUniversity of OtagoDunedinNew Zealand

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