International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Highlights • Sequencing results were in agreement for biologically conserved positions.• For biologically variable positions, sequencing depth impacted precision.• Results were biased by the algorithm used to align reads to the reference.

[1]  T. Thomas,et al.  GemSIM: general, error-model based simulator of next-generation sequencing data , 2012, BMC Genomics.

[2]  Mehrdad Hajibabaei,et al.  Next‐generation sequencing technologies for environmental DNA research , 2012, Molecular ecology.

[3]  B. Haas,et al.  Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. , 2011, Genome research.

[4]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[5]  Philip Hugenholtz,et al.  Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data , 2013, PLoS Comput. Biol..

[6]  Martin Kircher,et al.  High‐throughput DNA sequencing – concepts and limitations , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.

[7]  P. Baldrian,et al.  The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses , 2013, PloS one.

[8]  S. Abbott,et al.  16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls , 2007, Journal of Clinical Microbiology.

[9]  R. Borrow,et al.  Contamination and Sensitivity Issues with a Real-Time Universal 16S rRNA PCR , 2000, Journal of Clinical Microbiology.

[10]  A. Klindworth,et al.  Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies , 2012, Nucleic acids research.

[11]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[12]  K. Kakinuma,et al.  Phylogenetic Analysis of Salmonella, Shigella, and Escherichia coli Strains on the Basis of the gyrB Gene Sequence , 2002, Journal of Clinical Microbiology.

[13]  Lynn K. Carmichael,et al.  Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research , 2012, PloS one.

[14]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[15]  Norman R. Pace,et al.  Specific Ribosomal DNA Sequences from Diverse Environmental Settings Correlate with Experimental Contaminants , 1998, Applied and Environmental Microbiology.

[16]  Heng Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[17]  Stuart M. Brown,et al.  Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes , 2010, Applied and Environmental Microbiology.

[18]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[19]  Marc Salit,et al.  Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing , 2012, PloS one.

[20]  Philip Hugenholtz,et al.  A renaissance for the pioneering 16S rRNA gene. , 2008, Current opinion in microbiology.

[21]  Rob Knight,et al.  Bayesian community-wide culture-independent microbial source tracking , 2011, Nature Methods.