title: Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package.
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.
authors.affiliation: Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand. blair.lawley@otago.ac.nz.
authors.forename: Blair
authors.initials: B
authors.lastname: Lawley
authors.affiliation: Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
authors.forename: Gerald W
authors.initials: GW
authors.lastname: Tannock
mesh_terms: D000465:Algorithms; D044822:Biodiversity; D019295:Computational Biology / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012984:Software; D064878:Web Browser
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA gene; Bioinformatics; High-throughput sequencing; Microbial ecology; Operational taxonomic unit (OTU); QIIME; Sequence analysis