Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species
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Acinas, 2004, Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons, J Bacteriol, 186, 2629, 10.1128/JB.186.9.2629-2635.2004
Alexander, 2002, Phylogeny of green sulfur bacteria on the basis of gene sequences of 16S rRNA and of the Fenna-Matthews-Olson protein, Arch Microbiol, 178, 131, 10.1007/s00203-002-0432-4
Altschul, 1990, Basic local alignment search tool, J Mol Biol, 215, 403, 10.1016/S0022-2836(05)80360-2
Bosshard, 2006, 16S rRNA gene sequencing versus the API 20 NE system and the VITEK 2 ID-GNB card for identification of nonfermenting Gram-negative bacteria in the clinical laboratory, J Clin Microbiol, 44, 1359, 10.1128/JCM.44.4.1359-1366.2006
Brenner, 1969, Batch procedure for thermal elution of DNA from hydroxyapatite, Anal Biochem, 28, 447, 10.1016/0003-2697(69)90199-7
Chenna, 2003, Multiple sequence alignment with the clustal series of programs, Nucleic Acids Res, 31, 3497, 10.1093/nar/gkg500
Clarridge, 2004, Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases, Clin Microbiol Rev, 17, 840, 10.1128/CMR.17.4.840-862.2004
DeSantis, 2006, Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with arb, Appl Environ Microbiol, 72, 5069, 10.1128/AEM.03006-05
Fournier, 2009, Current knowledge on phylogeny and taxonomy of Rickettsia spp., Ann N Y Acad Sci, 1166, 1, 10.1111/j.1749-6632.2009.04528.x
Fox, 1977, Classification of methanogenic bacteria by 16S ribosomal RNA characterization, Proc Natl Acad Sci U S A, 74, 4537, 10.1073/pnas.74.10.4537
Fox, 1992, How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity, Int J Syst Bacteriol, 42, 166, 10.1099/00207713-42-1-166
Goujon, 2010, A new bioinformatics analysis tools framework at EMBL-EBI, Nucleic Acids Res, 38, W695, 10.1093/nar/gkq313
Hugenholtz, 1998, Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity, J Bacteriol, 180, 4765, 10.1128/JB.180.18.4765-4774.1998
Huse, 2008, Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing, PLoS Genet, 4, e1000255, 10.1371/journal.pgen.1000255
Janda, 2007, 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls, J Clin Microbiol, 45, 2761, 10.1128/JCM.01228-07
Johnson, 1991, DNA reassociation experiments, Nucleic Acid Techniques in Bacterial Systematics, 21
Kim, 2012, Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species, Int J Syst Evol Microbiol, 62, 716, 10.1099/ijs.0.038075-0
Ludwig, 2001, Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics, Bergey’s Manual of Systematic Bacteriology, vol. 1, 49, 10.1007/978-0-387-21609-6_8
Ludwig, 2004, arb: a software environment for sequence data, Nucleic Acids Res, 32, 1363, 10.1093/nar/gkh293
Mignard, 2006, 16S rRNA sequencing in routine bacterial identification: a 30-month experiment, J Microbiol Methods, 67, 574, 10.1016/j.mimet.2006.05.009
Morgulis, 2008, Database indexing for production Megablast searches, Bioinformatics, 24, 1757, 10.1093/bioinformatics/btn322
Olsen, 1995, Rejection of Clostridium putrificum and conservation of Clostridium botulinum and Clostridium sporogenes. Request for an Opinion, Int J Syst Bacteriol, 45, 414, 10.1099/00207713-45-2-414
Parte, 2014, LPSN–list of prokaryotic names with standing in nomenclature, Nucleic Acids Res, 42, D613, 10.1093/nar/gkt1111
Pei, 2010, Diversity of 16S rRNA genes within individual prokaryotic genomes, Appl Environ Microbiol, 76, 3886, 10.1128/AEM.02953-09
Quast, 2013, The silva ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res, 41, D590, 10.1093/nar/gks1219
Rosselló-Mora, 2003, Opinion: the species problem, can we achieve a universal concept?, Syst Appl Microbiol, 26, 323, 10.1078/072320203322497347
Roth, 2003, Phylogeny of the genus Nocardia based on reassessed 16S rRNA gene sequences reveals underspeciation and division of strains classified as Nocardia asteroides into three established species and two unnamed taxons, J Clin Microbiol, 41, 851, 10.1128/JCM.41.2.851-856.2003
Sentausa, 2013, Advantages and limitations of genomics in prokaryotic taxonomy, Clin Microbiol Infect, 19, 790, 10.1111/1469-0691.12181
Stackebrandt, 2006, Taxonomic parameters revisited: tarnished gold standards, Microbiol Today, 33, 152
Stackebrandt, 1994, Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology, Int J Syst Bacteriol, 44, 846, 10.1099/00207713-44-4-846
Stackebrandt, 2002, Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology, Int J Syst Evol Microbiol, 52, 1043
Tamura, 2011, mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol, 28, 2731, 10.1093/molbev/msr121
Tindall, 2010, Notes on the characterization of prokaryote strains for taxonomic purposes, Int J Syst Evol Microbiol, 60, 249, 10.1099/ijs.0.016949-0
Vandamme, 1996, Polyphasic taxonomy, a consensus approach to bacterial systematics, Microbiol Rev, 60, 407, 10.1128/MMBR.60.2.407-438.1996